Alignments for a candidate for sdaB in Nocardiopsis baichengensis YIM 90130

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Nocardiopsis baichengensis YIM 90130

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_017555996.1 C892_RS0103010 L-serine ammonia-lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>NCBI__GCF_000341205.1:WP_017555996.1
          Length = 456

 Score =  549 bits (1415), Expect = e-161
 Identities = 285/458 (62%), Positives = 332/458 (72%), Gaps = 2/458 (0%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           MSLSVFDLFK+GIGPSSSHTVGPMRAA  F   LR   +L     V+  L+GSLGATG G
Sbjct: 1   MSLSVFDLFKVGIGPSSSHTVGPMRAAYLFTIRLRASGVLPRVAGVRCGLFGSLGATGHG 60

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIRKPL 120
           HGS  AV+LGL+GE P  VD  +    ++A++  G L LLGEH I F+    +    + L
Sbjct: 61  HGSVTAVVLGLQGEQPHIVDPVSAGPGVRAVQEEGVLALLGEHKIAFSLDDVVLHRNERL 120

Query: 121 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDL 180
            FH NGM+F AFD  G  V  REYYSVGGGFV+DE  AG   +VED T   +PF++ ++L
Sbjct: 121 PFHSNGMVFEAFDDRGRTVDRREYYSVGGGFVLDEDEAGRPVLVEDGTATPYPFRTGEEL 180

Query: 181 LGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240
           L H    GL +S VML NE   R   E R GLL IW VM +CV  G    G+LPGGL+V+
Sbjct: 181 LAHTRRTGLPVSGVMLANERVRRTGDEVREGLLHIWSVMGECVDRGMSTSGVLPGGLRVR 240

Query: 241 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV 300
           RRA  L  +L         D L+ L+WV L+ALAVNEENA GGRVVTAPTNGAAGI+PAV
Sbjct: 241 RRAGGLRARL--EAGGGDDDALAALEWVTLFALAVNEENAAGGRVVTAPTNGAAGIVPAV 298

Query: 301 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360
           LHY   F+P    + VVRFLLTA AIGIL+KENASISGAEVGCQGEVG ACSMAA  L E
Sbjct: 299 LHYARDFLPSFGSEAVVRFLLTAGAIGILFKENASISGAEVGCQGEVGSACSMAAAGLAE 358

Query: 361 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH 420
           V+GG+ +QVENAAEIG+EHNLGLTCDP+GGLVQ+PCIERNA+ +VKAI A RMA+RGDG 
Sbjct: 359 VIGGTPEQVENAAEIGLEHNLGLTCDPVGGLVQIPCIERNAVAAVKAITAARMAVRGDGR 418

Query: 421 HFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           H VSLD  I TMRQTGADMK KYKETARGGLA+N++EC
Sbjct: 419 HHVSLDNAITTMRQTGADMKDKYKETARGGLALNVVEC 456


Lambda     K      H
   0.320    0.136    0.401 

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: 734
Number of extensions: 30
Number of successful extensions: 3
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: 458
Length of database: 456
Length adjustment: 33
Effective length of query: 425
Effective length of database: 423
Effective search space:   179775
Effective search space used:   179775
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_017555996.1 C892_RS0103010 (L-serine ammonia-lyase)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.150737.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-serine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-201  656.4   0.0   1.3e-201  656.2   0.0    1.0  1  NCBI__GCF_000341205.1:WP_017555996.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341205.1:WP_017555996.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  656.2   0.0  1.3e-201  1.3e-201       2     450 .]       4     453 ..       3     453 .. 0.98

  Alignments for each domain:
  == domain 1  score: 656.2 bits;  conditional E-value: 1.3e-201
                             TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelp 74 
                                           svfdlfk+GiGPssshtvGPm+aa+ f  +l+  g l +v+ v+  l+Gsl++tG+Gh++ +av+lGl+Ge+p
  NCBI__GCF_000341205.1:WP_017555996.1   4 SVFDLFKVGIGPSSSHTVGPMRAAYLFTIRLRASGVLPRVAGVRCGLFGSLGATGHGHGSVTAVVLGLQGEQP 76 
                                           9************************************************************************ PP

                             TIGR00720  75 eevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGG 147
                                           + vd  s+   +++v+ee++l+l+++++i f+l++ +  ++e lp+h ng+ ++a+d+ g+++ +++yysvGG
  NCBI__GCF_000341205.1:WP_017555996.1  77 HIVDPVSAGPGVRAVQEEGVLALLGEHKIAFSLDDVVLHRNERLPFHSNGMVFEAFDDRGRTVDRREYYSVGG 149
                                           ********************************87766666********************************* PP

                             TIGR00720 148 Gfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeec 218
                                           Gf++de+e+++    e+    pypf++ +ell++ +++gl +s v+l+ne + r+ +evr+ ll+iw+vm ec
  NCBI__GCF_000341205.1:WP_017555996.1 150 GFVLDEDEAGRPVLVEDgtATPYPFRTGEELLAHTRRTGLPVSGVMLANERVRRTGDEVREGLLHIWSVMGEC 222
                                           *********998766665699**************************************************** PP

                             TIGR00720 219 ierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagi 291
                                           ++rg+++ gvlpGgl+v+rra  l+++l+a      d la+l+wv+l+alavneenaaGgrvvtaPtnGaagi
  NCBI__GCF_000341205.1:WP_017555996.1 223 VDRGMSTSGVLPGGLRVRRRAGGLRARLEAGGGD-DDALAALEWVTLFALAVNEENAAGGRVVTAPTNGAAGI 294
                                           ****************************998877.599*********************************** PP

                             TIGR00720 292 iPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqv 364
                                           +Pavl+y++ f ++  +e+vvrflltagaiGil+kenasisgaevGCqgevG+acsmaaaglae++ggtpeqv
  NCBI__GCF_000341205.1:WP_017555996.1 295 VPAVLHYARDFLPSFGSEAVVRFLLTAGAIGILFKENASISGAEVGCQGEVGSACSMAAAGLAEVIGGTPEQV 367
                                           ************************************************************************* PP

                             TIGR00720 365 enaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkak 437
                                           enaaei++ehnlGltCdPvgGlvqiPCierna+aavkai aar+a+++dg+++vsld+ i tmr+tG+dmk k
  NCBI__GCF_000341205.1:WP_017555996.1 368 ENAAEIGLEHNLGLTCDPVGGLVQIPCIERNAVAAVKAITAARMAVRGDGRHHVSLDNAITTMRQTGADMKDK 440
                                           ************************************************************************* PP

                             TIGR00720 438 yketskgGlavkv 450
                                           yket++gGla +v
  NCBI__GCF_000341205.1:WP_017555996.1 441 YKETARGGLALNV 453
                                           **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (456 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 24.91
//
[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 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