Alignments for a candidate for putA in Croceitalea dokdonensis DOKDO 023

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Croceitalea dokdonensis DOKDO 023

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_054560547.1 I595_RS16455 L-glutamate gamma-semialdehyde dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>NCBI__GCF_001306415.1:WP_054560547.1
          Length = 542

 Score =  504 bits (1298), Expect = e-147
 Identities = 270/541 (49%), Positives = 351/541 (64%), Gaps = 9/541 (1%)

Query: 30  YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89
           ++VP   NEP   YA G+P+R+ + +   +   N  + VPL +  +E+K+ ++ T S P 
Sbjct: 6   FQVPTAINEPILSYAPGTPERENVLKQY-KAFYNGKMEVPLYVGSQEIKTGTTETMSPPH 64

Query: 90  SHGPVAT-YSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148
            H  V   Y  A  K  Q AI+S L +R +WA+  +  RA++FLKAA+LI+  YR  + A
Sbjct: 65  DHQHVVGHYHVADKKITQDAIDSCLASRAAWANLTWEQRAAIFLKAAELIAGPYRAKINA 124

Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208
            TM  Q K   QAEID+A E  DF RF V+Y   +Y +QP   A G+WNRVEYRPLEGFV
Sbjct: 125 ATMIAQSKTIHQAEIDAACEFIDFLRFNVEYMSQIYEEQP-ESAAGIWNRVEYRPLEGFV 183

Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268
           YAI+PFNFTAI GNL  + A+MGNVV+WKPS S + S  ++  +  EAGLP  VI  V G
Sbjct: 184 YAITPFNFTAIAGNLPASAAMMGNVVLWKPSDSQVFSAKIIMDVFKEAGLPDGVINMVMG 243

Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328
           +   +T+TVL + +F+ LHFTGST+VF+ L+ QI   +    Y++YPRIVGETGGK+F +
Sbjct: 244 DPVMITETVLSNANFSGLHFTGSTHVFKELWKQIGQNIHT--YKTYPRIVGETGGKDFII 301

Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLK-VGPPS 387
            H +A     A   VRGAFE+QGQKCSA SRVY+  S +D+ L  V  + +S    G P 
Sbjct: 302 AHPTAKPEQVATAIVRGAFEFQGQKCSAASRVYLPKSTSDAILSLVKKDMESFNPPGSPE 361

Query: 388 DFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHP 447
           D +NF   VIHEASF KLA  ID+AK D   E+ AGG YD SKG++I+PTV  T +P + 
Sbjct: 362 DMSNFITAVIHEASFDKLAHYIDQAKADENAEIYAGGGYDKSKGYFIEPTVILTKDPKYT 421

Query: 448 LLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRN 507
            +  ELFGP++ +Y Y D    D+ +  + +D T EY LTG+V ++DR A+  A   L+N
Sbjct: 422 TMYTELFGPVVTIYVYND---QDWGKTLKLVDETSEYALTGAVLSRDRYAIDEATKALQN 478

Query: 508 AAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAY 567
            AGNFYIN K TGAVVGQQPFGGARASGTNDKAGS   L R+VS R IKE FV      Y
Sbjct: 479 CAGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSAQNLLRWVSPRLIKETFVTPEDYRY 538

Query: 568 P 568
           P
Sbjct: 539 P 539


Lambda     K      H
   0.316    0.130    0.379 

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: 849
Number of extensions: 33
Number of successful extensions: 7
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: 572
Length of database: 542
Length adjustment: 36
Effective length of query: 536
Effective length of database: 506
Effective search space:   271216
Effective search space used:   271216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_054560547.1 I595_RS16455 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.3573851.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-233  762.1   0.8   1.7e-233  761.9   0.8    1.0  1  NCBI__GCF_001306415.1:WP_054560547.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001306415.1:WP_054560547.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  761.9   0.8  1.7e-233  1.7e-233       2     531 ..      13     540 ..      12     542 .] 0.99

  Alignments for each domain:
  == domain 1  score: 761.9 bits;  conditional E-value: 1.7e-233
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           neP+ +++pg++er+ + k+ k + + ++e+Pl +g +e +k++ + ++  P+dhq+++++ + a+++  ++a
  NCBI__GCF_001306415.1:WP_054560547.1  13 NEPILSYAPGTPERENVLKQYKAFYNGKMEVPLYVGSQE-IKTGTTETMSPPHDHQHVVGHYHVADKKITQDA 84 
                                           9************************************99.77787899999********************** PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           +++ l+++  W++l +++raaiflkaa+l++g+yr++i+aatm++qskt++qaeida++e idf+rfnv+y +
  NCBI__GCF_001306415.1:WP_054560547.1  85 IDSCLASRAAWANLTWEQRAAIFLKAAELIAGPYRAKINAATMIAQSKTIHQAEIDAACEFIDFLRFNVEYMS 157
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           +++e qP +sa g +n+veyrpleGfv+ai+Pfnftaia+nl+++ a+mGnvv+WkPs+ +v+s+ ++m +++
  NCBI__GCF_001306415.1:WP_054560547.1 158 QIYEEQP-ESAAGIWNRVEYRPLEGFVYAITPFNFTAIAGNLPASAAMMGNVVLWKPSDSQVFSAKIIMDVFK 229
                                           *******.9**************************************************************** PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293
                                           eaGlP gvin+v +d+v+++++vl++ ++++lhftGst+vfkelwk++ +n+++y+++PrivGetGGkdf+++
  NCBI__GCF_001306415.1:WP_054560547.1 230 EAGLPDGVINMVMGDPVMITETVLSNANFSGLHFTGSTHVFKELWKQIGQNIHTYKTYPRIVGETGGKDFIIA 302
                                           ************************************************************************* PP

                             TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvk.vgdvddlssfmgavideks 365
                                           hp+a+ e+v++a++rgafe+qGqkcsaasr+y+pks+++ + + +++++++ +  g ++d+s+f++avi+e s
  NCBI__GCF_001306415.1:WP_054560547.1 303 HPTAKPEQVATAIVRGAFEFQGQKCSAASRVYLPKSTSDAILSLVKKDMESFNpPGSPEDMSNFITAVIHEAS 375
                                           ************************************************9999835899*************** PP

                             TIGR01236 366 fakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeile 438
                                           f+k+ ++i++ak+d  + ei aGG yd+skGyf+ePtv+++kdPk  +m +e+fGPv+t+yvy+d+ + ++l+
  NCBI__GCF_001306415.1:WP_054560547.1 376 FDKLAHYIDQAKADE-NAEIYAGGGYDKSKGYFIEPTVILTKDPKYTTMYTELFGPVVTIYVYNDQDWGKTLK 447
                                           *************87.9******************************************************** PP

                             TIGR01236 439 vvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrf 511
                                           +vd+ts+yaltGav+++dr ai ea+k+l+++aGnfyindk+tGavvgqqpfGGar+sGtndkaG++++llr+
  NCBI__GCF_001306415.1:WP_054560547.1 448 LVDETSEYALTGAVLSRDRYAIDEATKALQNCAGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSAQNLLRW 520
                                           ************************************************************************* PP

                             TIGR01236 512 vsarsiketfkeltdfkypy 531
                                           vs+r iketf++++d++yp+
  NCBI__GCF_001306415.1:WP_054560547.1 521 VSPRLIKETFVTPEDYRYPF 540
                                           ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (542 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 34.54
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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