Alignments for a candidate for gcvT in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Phaeobacter inhibens BS107

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate GFF3865 PGA1_78p00290 aminomethyltransferase GcvT

Query= reanno::WCS417:GFF4369
         (374 letters)



>FitnessBrowser__Phaeo:GFF3865
          Length = 365

 Score =  346 bits (888), Expect = e-100
 Identities = 178/371 (47%), Positives = 244/371 (65%), Gaps = 7/371 (1%)

Query: 3   TETLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHLHTRDQAGLFDVSHMGQIRL 62
           T+   +TPL+ LH+ LG +MV FAG++MPVQYP+G+M EH   R++A LFDVSHMGQ+ L
Sbjct: 2   TDAPKRTPLYDLHVALGGKMVDFAGWEMPVQYPMGIMGEHKQCREKAALFDVSHMGQVIL 61

Query: 63  TGANAAKALETLVPVDILDLPVGMQRYAMFTNDQGGILDDLMVANLGNEELFLVVNAACK 122
            G N  + LE + P     L  G  RY  FTN+ GGI+DDL+V+N G +  F+VVNAA +
Sbjct: 62  RGDNVGEKLEAICPQAYATLKEGKARYGFFTNEDGGIMDDLIVSNAG-DHYFVVVNAALR 120

Query: 123 DQDLAHLRQHIGDQCTIEPLFEERALLALQGPAAVKVLARLAPEVTKMTFMQFATLRLLG 182
            QD+ H++ H+ D   +  +F+ RAL+A+QGPAA  V+  L P   +M FM+     + G
Sbjct: 121 HQDIPHMKAHL-DGVEVTEIFD-RALVAVQGPAAENVVGDLCPAAREMKFMETIVADIDG 178

Query: 183 VDCYVSRSGYTGEDGFEISVPAANAESLARSLLAETEVQAIGLGARDSLRLEAGLCLYGH 242
           V+C +SR GYTGEDG+EIS+P A+AE + +  LA  + +  GLGARDSLRLEAGLCLYG+
Sbjct: 179 VECRLSRLGYTGEDGYEISIPDADAERITKLFLAHDDCEPAGLGARDSLRLEAGLCLYGN 238

Query: 243 DMNTDTTPIEASLLWAISKARRADGARAGGFPGADTIFTQQQAGVSRKRVGLLPQERTPV 302
           D++  T+PIEASL WAI K R+ +    GGFPGAD I  +   G ++K VG+ P  R P 
Sbjct: 239 DIDQSTSPIEASLAWAIQKRRKEE----GGFPGADRIRKELADGAAKKLVGIKPSGRAPA 294

Query: 303 REGAQIVDADGTVIGSVCSGGFGSTLGGPLAMGYLDSAFIALDTEVSALVRGKKVPLRVS 362
           R+  +I  A+G  IG + SG FG T+GGP+AMGY+ +       +V  ++RGK     + 
Sbjct: 295 RQHVEIQCAEGNTIGEITSGCFGPTVGGPVAMGYVAAPHGKAGEQVKLIIRGKAHDAEIV 354

Query: 363 KMPFVPQRYYR 373
            +PFV Q Y R
Sbjct: 355 ALPFVTQNYKR 365


Lambda     K      H
   0.321    0.137    0.398 

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: 404
Number of extensions: 17
Number of successful extensions: 4
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: 374
Length of database: 365
Length adjustment: 30
Effective length of query: 344
Effective length of database: 335
Effective search space:   115240
Effective search space used:   115240
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 GFF3865 PGA1_78p00290 (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.22702.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.2e-104  333.5   0.0   8.4e-104  333.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3865  PGA1_78p00290 aminomethyltransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3865  PGA1_78p00290 aminomethyltransferase GcvT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.3   0.0  8.4e-104  8.4e-104       2     361 ..       6     360 ..       5     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 333.3 bits;  conditional E-value: 8.4e-104
                          TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqy.kslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaL 76 
                                        krtpLydlh+ lggk+vdfaGwe+Pvqy  +++ eh+  r+ka lfDvshmg+v l+G+++ + L+ + ++  + L
  lcl|FitnessBrowser__Phaeo:GFF3865   6 KRTPLYDLHVALGGKMVDFAGWEMPVQYpMGIMGEHKQCREKAALFDVSHMGQVILRGDNVGEKLEAICPQAYATL 81 
                                        89**************************55889******************************************* PP

                          TIGR00528  77 tkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkak 152
                                         +Gka+y  + n +GG++DDliv + g+   + +vvnaa +++D  ++k hl++  ++ +   + +l+a+qGP a+
  lcl|FitnessBrowser__Phaeo:GFF3865  82 KEGKARYGFFTNEDGGIMDDLIVSNAGDH--YFVVVNAALRHQDIPHMKAHLDGV-EVTE-IFDRALVAVQGPAAE 153
                                        *************************9998..99*******************864.4444.44569********** PP

                          TIGR00528 153 tiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtL 228
                                        +++ dl  + + ++k +  +  a++ + ++ ++r GytGedG+ei++++ +a  + k ++++    P GLgarD+L
  lcl|FitnessBrowser__Phaeo:GFF3865 154 NVVGDLCPA-AREMKFMETI-VADIDGVECRLSRLGYTGEDGYEISIPDADAERITKLFLAHDDCEPAGLGARDSL 227
                                        *****9975.6789988888.9****************************************************** PP

                          TIGR00528 229 rleagmaLyGqeldeeitPleaglgwvvkker.kksdfiGravleeqkengtekklvGlemlekgiarnelkvllt 303
                                        rleag++LyG+++d++++P+ea+l w+++k r ++  f G + + +  ++g+ kklvG++   +  ar+++++  +
  lcl|FitnessBrowser__Phaeo:GFF3865 228 RLEAGLCLYGNDIDQSTSPIEASLAWAIQKRRkEEGGFPGADRIRKELADGAAKKLVGIKPSGRAPARQHVEIQCA 303
                                        *****************************99845679*************************************** PP

                          TIGR00528 304 ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                        +g +++G +tsG + Pt+g  +a++yv     k G++++  +r+k  ++++v  +fv 
  lcl|FitnessBrowser__Phaeo:GFF3865 304 EG-NTIGEITSGCFGPTVGGPVAMGYVAAPHGKAGEQVKLIIRGKAHDAEIVALPFVT 360
                                        **.899************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (365 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: 00:00:00.01
# Mc/sec: 8.49
//
[ok]

This GapMind analysis is from Sep 17 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