Alignments for a candidate for gcvT in Algiphilus aromaticivorans DG1253

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Algiphilus aromaticivorans DG1253

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_043768713.1 U743_RS12500 glycine cleavage system aminomethyltransferase GcvT

Query= reanno::Koxy:BWI76_RS23880
         (364 letters)



>NCBI__GCF_000733765.1:WP_043768713.1
          Length = 359

 Score =  358 bits (920), Expect = e-104
 Identities = 194/363 (53%), Positives = 243/363 (66%), Gaps = 9/363 (2%)

Query: 3   QQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRI 62
           ++T L   H   GAR++DF GW MP+ Y SQ++EHHAVR  AG+FDV HM  VD  G   
Sbjct: 5   KKTVLHPLHAEAGARLIDFGGWEMPVQYRSQVEEHHAVRKAAGIFDVGHMRAVDIEGKDA 64

Query: 63  REFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREKDL 122
             FLRYLLANDVAKL   G+ALYS ML   GGV DDLI+Y ++E  +R V+N+AT   DL
Sbjct: 65  EAFLRYLLANDVAKLE-DGRALYSCMLDERGGVKDDLIIYRVAEGSYRAVLNAATAMADL 123

Query: 123 AWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAGDL 182
            W+ +Q       I +R+D +++A+QGP+A E    L   A  +A   +KPF   +AGD+
Sbjct: 124 DWMGEQRFG-DCRIHLREDRTIVALQGPKAAEILPKLVDGAAAEAALALKPFRCTEAGDV 182

Query: 183 FIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEMDE 242
           FI  TGYTGE G+EI LP EQA DFWR  +DAG +PCGLGARDTLRLEAGMNLYGQ+M E
Sbjct: 183 FIGRTGYTGEDGFEIVLPVEQAQDFWRAAVDAGAEPCGLGARDTLRLEAGMNLYGQDMSE 242

Query: 243 GVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRFSD 302
              P  A + WT+A EP DRDFIGR ALE    +   ++VGLV+  +GV+RG +PVRF  
Sbjct: 243 DTFPAEAGLSWTVALEPADRDFIGRAALE--NAQPDRRMVGLVLEGRGVMRGHMPVRFP- 299

Query: 303 ADGNQKEGIITSGTFSPTLGYSIALARV-PEGIGETAVVQIRNREMPVKVTKPVFVRNGK 361
              N  +G  TSG+ +PT+G SIALARV     GE A + IR R +PV+V KP FVRNG+
Sbjct: 300 ---NGADGETTSGSHAPTMGCSIALARVQSHAEGEAAEICIRGRWLPVRVVKPPFVRNGQ 356

Query: 362 AVV 364
             V
Sbjct: 357 VRV 359


Lambda     K      H
   0.320    0.137    0.407 

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: 384
Number of extensions: 18
Number of successful extensions: 6
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: 364
Length of database: 359
Length adjustment: 29
Effective length of query: 335
Effective length of database: 330
Effective search space:   110550
Effective search space used:   110550
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: 49 (23.5 bits)

Align candidate WP_043768713.1 U743_RS12500 (glycine cleavage system aminomethyltransferase GcvT)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# 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/TIGR00528.hmm
# target sequence database:        /tmp/gapView.3335859.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-123  398.5   0.0   1.4e-123  398.3   0.0    1.0  1  NCBI__GCF_000733765.1:WP_043768713.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000733765.1:WP_043768713.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.3   0.0  1.4e-123  1.4e-123       1     362 []       4     354 ..       4     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 398.3 bits;  conditional E-value: 1.4e-123
                             TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDv 73 
                                           lk+t L+ lh e g++l+df+Gwe+Pvqy s++eeh+avr++aG+fDv hm  v+++G+++ +fL++llanDv
  NCBI__GCF_000733765.1:WP_043768713.1   4 LKKTVLHPLHAEAGARLIDFGGWEMPVQYRSQVEEHHAVRKAAGIFDVGHMRAVDIEGKDAEAFLRYLLANDV 76 
                                           69*********************************************************************** PP

                             TIGR00528  74 daLtkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllal 146
                                           ++L  G+a+ys +l   GGv DDli+y+ +e   ++ v+naata  Dl+w+ e+  ++  ++ l+++ +++al
  NCBI__GCF_000733765.1:WP_043768713.1  77 AKLEDGRALYSCMLDERGGVKDDLIIYRVAEG-SYRAVLNAATAMADLDWMGEQRFGDCRIH-LREDRTIVAL 147
                                           *******************************9.********************999998875.788899**** PP

                             TIGR00528 147 qGPkaktiledlldkaveg....lkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveay 215
                                           qGPka++il +l+d a+ +    lk+f   +++++     +i rtGytGedGfei+++ e+a+++w++ v+a 
  NCBI__GCF_000733765.1:WP_043768713.1 148 QGPKAAEILPKLVDGAAAEaalaLKPFRCTEAGDV-----FIGRTGYTGEDGFEIVLPVEQAQDFWRAAVDA- 214
                                           *************9887766778*******99999.....********************************. PP

                             TIGR00528 216 gvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlem 288
                                           g  P+GLgarDtLrleagm+LyGq++ e++ P eagl+w+v++e++++dfiGra+le+    + ++++vGl++
  NCBI__GCF_000733765.1:WP_043768713.1 215 GAEPCGLGARDTLRLEAGMNLYGQDMSEDTFPAEAGLSWTVALEPADRDFIGRAALENA---QPDRRMVGLVL 284
                                           ********************************************************865...46789****** PP

                             TIGR00528 289 lekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                             +g++r +++v+++ng    G  tsG+ +Pt+g +iala+v+   +  G+ +e+ +r++ ++++vvk++fvr
  NCBI__GCF_000733765.1:WP_043768713.1 285 EGRGVMRGHMPVRFPNG--ADGETTSGSHAPTMGCSIALARVQ--SHAEGEAAEICIRGRWLPVRVVKPPFVR 353
                                           *****************..89**********************..7888***********************9 PP

                             TIGR00528 362 s 362
                                           +
  NCBI__GCF_000733765.1:WP_043768713.1 354 N 354
                                           6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (359 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: 20.06
//
[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