Alignments for a candidate for gcvT in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Acidovorax sp. GW101-3H11

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate Ac3H11_165 Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5556
         (374 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_165
          Length = 380

 Score =  450 bits (1158), Expect = e-131
 Identities = 235/379 (62%), Positives = 281/379 (74%), Gaps = 7/379 (1%)

Query: 2   STEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIR 61
           +T  LL TPL+ALH+ELGARMVPFAGY MPVQYP G+M EH HTR  AGLFDVSHMGQ++
Sbjct: 3   ATAPLLTTPLNALHIELGARMVPFAGYSMPVQYPAGLMAEHVHTRTAAGLFDVSHMGQLK 62

Query: 62  LTGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLG----NDELFLVV 117
           L GA AA A ETL+PVD+IDLPVG QRY +   + G ++DDLM  N G       LF++V
Sbjct: 63  LIGADAAAAFETLMPVDVIDLPVGKQRYGLLLTDEGTVIDDLMFFNQGVVDGEPTLFVIV 122

Query: 118 NAACKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQR 177
           N ACK  D+AH+ A IG +C + P+ +  ALLALQGP AVT LARLAP V K+ FM    
Sbjct: 123 NGACKVGDIAHIEARIGQRCQVVPMPD-HALLALQGPQAVTALARLAPGVEKLVFMTGGA 181

Query: 178 VTLLGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGL 237
            ++ G DC+V+RSGYTGEDGFEISVP A+A+ LARALLA+PEV  IGLGAR+SLRLEAGL
Sbjct: 182 FSIAGCDCFVTRSGYTGEDGFEISVPTAQADTLARALLAQPEVQPIGLGARNSLRLEAGL 241

Query: 238 CLYGHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQ--QQGGVKRKRVGLL 295
           CLYG+D++T TTP EA+L WAI KVRR  GARAGGFPGAE V AQ      + RKRVGL+
Sbjct: 242 CLYGNDIDTTTTPPEAALNWAIQKVRRTGGARAGGFPGAEKVLAQIDNPATLPRKRVGLV 301

Query: 296 PQERTPVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGK 355
             ER PVRE  E+ ++ G+ IG V SG  GPT+  P+AMGY+  A+ A+ T V AIVRGK
Sbjct: 302 ALERVPVREHTELQSQDGQKIGEVTSGLLGPTVNEPVAMGYVLPAFAAIGTRVNAIVRGK 361

Query: 356 KVPLLVSKMPFVPQRYYRG 374
            VP+ V  MPFVP  Y+RG
Sbjct: 362 AVPMEVRAMPFVPANYFRG 380


Lambda     K      H
   0.321    0.138    0.406 

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: 500
Number of extensions: 24
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: 380
Length adjustment: 30
Effective length of query: 344
Effective length of database: 350
Effective search space:   120400
Effective search space used:   120400
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: 50 (23.9 bits)

Align candidate Ac3H11_165 (Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10))
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.22223.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    2.5e-97  312.0   0.0    2.8e-97  311.8   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165  Aminomethyltransferase (glycine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165  Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.8   0.0   2.8e-97   2.8e-97       2     361 ..       8     374 ..       7     375 .. 0.93

  Alignments for each domain:
  == domain 1  score: 311.8 bits;  conditional E-value: 2.8e-97
                                       TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqy.kslieeheavrtkaGlfDvshmgkvelsGskslk 63 
                                                       tpL  lh elg+++v+faG+++Pvqy ++l+ eh  +rt+aGlfDvshmg+ +l G ++ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165   8 LTTPLNALHIELGARMVPFAGYSMPVQYpAGLMAEHVHTRTAAGLFDVSHMGQLKLIGADAAA 70 
                                                     579*************************6678******************************* PP

                                       TIGR00528  64 fLqrllanDvdaLtkGkaqysvllnaqGGvvDDlivykeged..n.rfllvvnaataekDlew 123
                                                     +++ l++ Dv  L++Gk +y  ll  +G v+DDl+ +++g    + ++ ++vn a+++ D ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165  71 AFETLMPVDVIDLPVGKQRYGLLLTDEGTVIDDLMFFNQGVVdgEpTLFVIVNGACKVGDIAH 133
                                                     *************************************9985423348999************* PP

                                       TIGR00528 124 lkehleeevtldtlskeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliar 186
                                                     ++ ++ +  ++  +  + +llalqGP+a t l  l    ve+l  +++  +  +a+ +++++r
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165 134 IEARIGQRCQVVPMP-DHALLALQGPQAVTALARLA-PGVEKLVFMTG-GAFSIAGCDCFVTR 193
                                                     *****9999998765.569***********999875.34565543333.3677888899**** PP

                                       TIGR00528 187 tGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPle 249
                                                     +GytGedGfei+v++ +a  l+++l++++ v+PiGLgar++Lrleag++LyG+++d ++tP e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165 194 SGYTGEDGFEISVPTAQADTLARALLAQPEVQPIGLGARNSLRLEAGLCLYGNDIDTTTTPPE 256
                                                     *************************************************************** PP

                                       TIGR00528 250 aglgwvvkker.....kksdfiGravleeqkengte..kklvGlemlekgiarnelkvlltng 305
                                                     a+l+w+++k r     +   f G +++  q +n +   +k+vGl+ le+   r++ ++  ++g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165 257 AALNWAIQKVRrtggaRAGGFPGAEKVLAQIDNPATlpRKRVGLVALERVPVREHTELQSQDG 319
                                                     *********99899888899***********998754488*******************9999 PP

                                       TIGR00528 306 ekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                                      +++G vtsG l Pt++  +a++yv   ++ iGt+++  vr+k v+++v  ++fv+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_165 320 -QKIGEVTSGLLGPTVNEPVAMGYVLPAFAAIGTRVNAIVRGKAVPMEVRAMPFVP 374
                                                     .9****************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (380 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: 7.09
//
[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