Alignments for a candidate for adiA in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas benzenivorans DSM 8628

Align Biosynthetic arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_090440327.1 BLS63_RS04420 arginine decarboxylase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1296
         (637 letters)



>NCBI__GCF_900100495.1:WP_090440327.1
          Length = 637

 Score = 1193 bits (3086), Expect = 0.0
 Identities = 595/637 (93%), Positives = 615/637 (96%)

Query: 1   MSVRRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDAGRVEVRPNGPTSSPIDLFEQVD 60
           MS RRTRKDDGSQWTVADSRSVYGIRHWGAGYFAIND GRVEVRPNGP S PIDLFEQVD
Sbjct: 1   MSARRTRKDDGSQWTVADSRSVYGIRHWGAGYFAINDRGRVEVRPNGPASMPIDLFEQVD 60

Query: 61  QLRKSGLSLPLLVRFPDILQDRVRQLTGAFDANIERLEYQSKYTALYPIKVNQQEAVIEN 120
           +LR+SGLSLPLLVRFPDILQDRVRQLTGAFDANI RLEYQS+YTALYPIKVNQQEAVIEN
Sbjct: 61  ELRQSGLSLPLLVRFPDILQDRVRQLTGAFDANIARLEYQSRYTALYPIKVNQQEAVIEN 120

Query: 121 IIATQNVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180
           IIATQ+VSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI
Sbjct: 121 IIATQDVSIGLEAGSKPELLAVLALAPKGGTIVCNGYKDREFIRLALMGQKLGHNVFIVI 180

Query: 181 EKESEVGLVIEEAASLKVKPQVGLRVRLSSLASSKWADTGGEKSKFGLSAAQLLSVVERF 240
           EKESEV LVIEEAA L+V PQ+GLRVRLSSLASSKWADTGGEKSKFGLSAAQL++VVERF
Sbjct: 181 EKESEVQLVIEEAAELRVAPQIGLRVRLSSLASSKWADTGGEKSKFGLSAAQLIAVVERF 240

Query: 241 RAAGLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRNLGLPVDHIDVGGGLGVDY 300
           RAA LDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELR LGLPVDHIDVGGGLGVDY
Sbjct: 241 RAAKLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRGLGLPVDHIDVGGGLGVDY 300

Query: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQSLPHPNIFSESGRSLTAHHAMLVVQVT 360
           DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQ LPHP+IFSESGRSLTAHHAMLVVQVT
Sbjct: 301 DGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQQLPHPHIFSESGRSLTAHHAMLVVQVT 360

Query: 361 DVEKHNDDVPKIDNKEELPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVATQYADGKL 420
           DVEKHND VP I+++  LPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVA QYA+GK+
Sbjct: 361 DVEKHNDAVPLIEDQASLPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVAAQYAEGKI 420

Query: 421 TLAQKALAEQCYFAVCRRLHNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480
           +L QKALAEQCYFAVCRRL+NSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA
Sbjct: 421 SLVQKALAEQCYFAVCRRLYNSLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWA 480

Query: 481 IGQVLPILPLHRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHGLNEGEDYLL 540
           IGQVLPILPL+RLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVH + EGEDYLL
Sbjct: 481 IGQVLPILPLNRLDEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHEVREGEDYLL 540

Query: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600
           GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL
Sbjct: 541 GIFLVGAYQEILGDMHNLFGDTDSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEEL 600

Query: 601 MTHYRDKCASARISAAERTQFLDALRLGLTRSSYLSS 637
           MTHYRDK ASA+IS  ERTQFLDALRLGLTRSSYL+S
Sbjct: 601 MTHYRDKVASAKISVRERTQFLDALRLGLTRSSYLAS 637


Lambda     K      H
   0.319    0.136    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1331
Number of extensions: 43
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 637
Length of database: 637
Length adjustment: 38
Effective length of query: 599
Effective length of database: 599
Effective search space:   358801
Effective search space used:   358801
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_090440327.1 BLS63_RS04420 (arginine decarboxylase)
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01273.hmm
# target sequence database:        /tmp/gapView.11919.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01273  [M=624]
Accession:   TIGR01273
Description: speA: arginine decarboxylase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-270  882.9   0.0   7.2e-270  882.7   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090440327.1  BLS63_RS04420 arginine decarboxy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090440327.1  BLS63_RS04420 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  882.7   0.0  7.2e-270  7.2e-270       1     623 [.      14     635 ..      14     636 .. 0.99

  Alignments for each domain:
  == domain 1  score: 882.7 bits;  conditional E-value: 7.2e-270
                                 TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqk 69 
                                               w++++s++vY+i++Wgagyfa+n++G+v+vrp+g   +  idl e v+++++ gl+lPllvrFpdilq+
  lcl|NCBI__GCF_900100495.1:WP_090440327.1  14 WTVADSRSVYGIRHWGAGYFAINDRGRVEVRPNGPA-SMPIDLFEQVDELRQSGLSLPLLVRFPDILQD 81 
                                               88999***************************9988.89****************************** PP

                                 TIGR01273  70 rikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasggkslGLEaGsKpEllialalaekpk 138
                                               r+++l+ aF+++i +leY+s+y+a+yPiKvnqq++v+e+++a+++ s+GLEaGsKpEll++lala  ++
  lcl|NCBI__GCF_900100495.1:WP_090440327.1  82 RVRQLTGAFDANIARLEYQSRYTALYPIKVNQQEAVIENIIATQDVSIGLEAGSKPELLAVLALAP-KG 149
                                               ******************************************************************.88 PP

                                 TIGR01273 139 avivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwas 207
                                                +ivcnGyKDre+i+lal+++klg++v+iviek++E++lvieea++l v P++GlRvrL+s +s+kwa+
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 150 GTIVCNGYKDREFIRLALMGQKLGHNVFIVIEKESEVQLVIEEAAELRVAPQIGLRVRLSSLASSKWAD 218
                                               99******************************************************************* PP

                                 TIGR01273 208 sgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvki 276
                                               +gGeksKFGLsa+q+++vv+++++++l++ ++llHfH+Gsqian++d+++g++Ea+r+y elr lG+++
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 219 TGGEKSKFGLSAAQLIAVVERFRAAKLDQGIRLLHFHMGSQIANLADYQHGFKEAIRYYGELRGLGLPV 287
                                               ********************************************************************* PP

                                 TIGR01273 277 evvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavlv 345
                                               +++dvGGGLgvdYdGt+s++++s+nY++++ya  vv +lke+c+++++p+P+i+sEsGR++tahha+lv
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 288 DHIDVGGGLGVDYDGTHSRNASSINYDMDDYAGVVVGMLKEFCDAQQLPHPHIFSESGRSLTAHHAMLV 356
                                               ********************************************************************* PP

                                 TIGR01273 346 aevleveeeeeeeaeeile.eeapeevkeleellkeideesaeelledavqlleeavelfklGkldlee 413
                                               ++v++ve++++   + i +    pe+v++l +ll+++d e+++e++++a+++++++++++++Gk++l +
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 357 VQVTDVEKHNDAV-PLIEDqASLPETVQWLVDLLGPTDIEMVTETYWRATHYMSDVAAQYAEGKISLVQ 424
                                               *********9995.333332579********************************************** PP

                                 TIGR01273 414 ralaeqlalailkkvke.leakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPlerL 481
                                               +alaeq++ a+++++ + l+a+++shr++ldel++kla+ky++n+s+FqslPD+W+i+q++PilPl+rL
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 425 KALAEQCYFAVCRRLYNsLKARQRSHRQVLDELNDKLADKYICNFSVFQSLPDTWAIGQVLPILPLNRL 493
                                               ***************999*************************************************** PP

                                 TIGR01273 482 dekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdt 550
                                               de+p rravl+DltCDsDGkik++v+eq+ie++lp+he+++ e+yllg+flvGAYqEiLgd+HnLFgdt
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 494 DEEPLRRAVLQDLTCDSDGKIKQYVDEQSIETSLPVHEVREGEDYLLGIFLVGAYQEILGDMHNLFGDT 562
                                               ********************************************************************* PP

                                 TIGR01273 551 eavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekkqvlelleaglsg 619
                                               ++v+++++++g+v+++ ie++dt+ed+l++v+++peel++++++kva+ak++ +e++q+l++l+ gl++
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 563 DSVNIYQNADGSVYHAGIETHDTIEDMLRYVHLSPEELMTHYRDKVASAKISVRERTQFLDALRLGLTR 631
                                               ********************************************************************* PP

                                 TIGR01273 620 ypYL 623
                                               ++YL
  lcl|NCBI__GCF_900100495.1:WP_090440327.1 632 SSYL 635
                                               ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (637 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.11
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources