Alignments for a candidate for gcvT in Thermithiobacillus tepidarius DSM 3134

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Thermithiobacillus tepidarius DSM 3134

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_028990024.1 G579_RS0109690 glycine cleavage system aminomethyltransferase GcvT

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



>NCBI__GCF_000423825.1:WP_028990024.1
          Length = 367

 Score =  374 bits (960), Expect = e-108
 Identities = 203/371 (54%), Positives = 257/371 (69%), Gaps = 17/371 (4%)

Query: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60
           M  +TPL++ H   GA+MVDF GW MPLHYGSQ++EHH VR DAG+FDVSHMT+VDFHG+
Sbjct: 1   MGLRTPLYDWHAAHGAKMVDFGGWDMPLHYGSQLEEHHQVRRDAGLFDVSHMTVVDFHGA 60

Query: 61  RIREFLRYLLANDVAKLT-VPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATRE 119
               FL+ LLANDVA++   PGKALYS ML  +GGV+DDLIVYF+  D +R+VVN+AT E
Sbjct: 61  EAGRFLQTLLANDVARIQQTPGKALYSCMLNETGGVVDDLIVYFIRPDCYRMVVNAATTE 120

Query: 120 KDLAWIAQQSESYGLEITVR--DDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFG- 176
           KDLAWI  Q   Y   + +R  DDL+++AVQGP+A+ K   +  +    AV+ +KPF G 
Sbjct: 121 KDLAWIESQRAHYAPSVDMRRRDDLAMLAVQGPQARAKTTVVLGEP---AVDALKPFTGG 177

Query: 177 ---VQAGDLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGM 233
              +   + F+A TGYTGE G+EI LPN  A    R LLDAGV+P GLGARDTLRLEAGM
Sbjct: 178 FFKIDGAEYFVARTGYTGEDGFEIMLPNTAAPGLARRLLDAGVRPAGLGARDTLRLEAGM 237

Query: 234 NLYGQEMDEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGT-EQLVGLVMTEKGVL 292
           NLYGQ+MDEG +PL +N+ WT+A + + RDFIGR ALE Q+  G    LVGLV+   G+ 
Sbjct: 238 NLYGQDMDEGTTPLESNLAWTVALKDS-RDFIGRAALETQQRAGVPRSLVGLVIPAGGIP 296

Query: 293 RGGLPVRFSDADGNQKEGIITSGTFSPTLGYSIALARVPEGI--GETAVVQIRNREMPVK 350
           R    V   DA+G Q  G ITSG+FSPTLG  IA ARV      G+   V+IR + +P +
Sbjct: 297 RAHQAV--LDAEGKQ-IGEITSGSFSPTLGLGIAFARVQGAFAPGDALAVEIRGKAVPAQ 353

Query: 351 VTKPVFVRNGK 361
           V +P FV+ G+
Sbjct: 354 VVRPPFVKQGQ 364


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: 440
Number of extensions: 20
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: 364
Length of database: 367
Length adjustment: 30
Effective length of query: 334
Effective length of database: 337
Effective search space:   112558
Effective search space used:   112558
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_028990024.1 G579_RS0109690 (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.4191709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-127  411.0   0.0   2.3e-127  410.8   0.0    1.0  1  NCBI__GCF_000423825.1:WP_028990024.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000423825.1:WP_028990024.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.8   0.0  2.3e-127  2.3e-127       3     361 ..       4     361 ..       2     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 410.8 bits;  conditional E-value: 2.3e-127
                             TIGR00528   3 rtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvda 75 
                                           rtpLyd h   g+k+vdf+Gw +P++y+s+ eeh+ vr +aGlfDvshm+ v+  G ++ +fLq llanDv++
  NCBI__GCF_000423825.1:WP_028990024.1   4 RTPLYDWHAAHGAKMVDFGGWDMPLHYGSQLEEHHQVRRDAGLFDVSHMTVVDFHGAEAGRFLQTLLANDVAR 76 
                                           9***********************************************************************9 PP

                             TIGR00528  76 L..tkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeev.tld.tlskeisll 144
                                           +  t+Gka+ys +ln  GGvvDDlivy    d  +++vvnaat+ekDl+w++ + ++ + ++d   ++++++l
  NCBI__GCF_000423825.1:WP_028990024.1  77 IqqTPGKALYSCMLNETGGVVDDLIVYFIRPD-CYRMVVNAATTEKDLAWIESQRAHYApSVDmRRRDDLAML 148
                                           84466*************************99.******************8765544314441356789*** PP

                             TIGR00528 145 alqGPkaktiled.lldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveayg 216
                                           a+qGP+a++     l + av++lk+f+++    + + + ++artGytGedGfei+++n  a  l+++l++a g
  NCBI__GCF_000423825.1:WP_028990024.1 149 AVQGPQARAKTTVvLGEPAVDALKPFTGG-FFKIDGAEYFVARTGYTGEDGFEIMLPNTAAPGLARRLLDA-G 219
                                           *****98776554156789999***9988.677777888********************************.* PP

                             TIGR00528 217 vkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGleml 289
                                           v+P GLgarDtLrleagm+LyGq++de +tPle++l w+v+++ + +dfiGra+le q+  g+ + lvGl++ 
  NCBI__GCF_000423825.1:WP_028990024.1 220 VRPAGLGARDTLRLEAGMNLYGQDMDEGTTPLESNLAWTVALK-DSRDFIGRAALETQQRAGVPRSLVGLVIP 291
                                           *******************************************.99*************************** PP

                             TIGR00528 290 ekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                           + gi+r +  vl ++g k++G +tsG++sPtLg  ia a+v+ +    G+ l ve+r+k v+++vv+++fv+
  NCBI__GCF_000423825.1:WP_028990024.1 292 AGGIPRAHQAVLDAEG-KQIGEITSGSFSPTLGLGIAFARVQ-GAFAPGDALAVEIRGKAVPAQVVRPPFVK 361
                                           *************9*9.9************************.78889**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (367 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.73
//
[ok]

This GapMind analysis is from Apr 09 2024. 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