Alignments for a candidate for gcvT in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Dinoroseobacter shibae DFL-12

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate 3609296 Dshi_2682 glycine cleavage system T protein (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1866
         (374 letters)



>FitnessBrowser__Dino:3609296
          Length = 361

 Score =  338 bits (866), Expect = 2e-97
 Identities = 189/368 (51%), Positives = 241/368 (65%), Gaps = 8/368 (2%)

Query: 6   LLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRLTGA 65
           L KTPLH LH+ELGA+MVPFA ++MPVQYP G+M EH   R+ A LFDVSHM Q+ +TG 
Sbjct: 2   LKKTPLHPLHLELGAKMVPFAWWEMPVQYPTGIMAEHAACREGAALFDVSHMCQMEITGD 61

Query: 66  NAAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAACKDQD 125
           + A ALE LVP  I  L  G  RY   T   GGI DDL+V       L++V NA+  DQD
Sbjct: 62  DPAAALERLVPGGITSLAPGQARYTQLTTGAGGIYDDLIVTR-DPGGLYVVANASMADQD 120

Query: 126 LAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKLLGVDC 185
           +  LR  + D CT+  + E+ AL+A+QGPAA  ++A L P    + FMQ A+    G D 
Sbjct: 121 VGLLRAGLPD-CTLR-VIEDHALIAVQGPAAAALVAGLVPAAEDLRFMQSAQAAWDGQDL 178

Query: 186 FVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLYGHDMN 245
            +SR GYTGEDGFEIS+PAT AEA ARAL+A   + A GLGARD+LR+EAGL LYG D++
Sbjct: 179 RLSRLGYTGEDGFEISLPATAAEAFARALIAGGAMPA-GLGARDTLRMEAGLPLYGQDID 237

Query: 246 TDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERTPVREG 305
             T+P EA L ++I K RRA+    GGFPGA  +  +   G +R+ VGL P+ R PVR G
Sbjct: 238 QGTSPPEAGLGFSIPKRRRAE----GGFPGAARILGELADGPARRLVGLRPEGRAPVRAG 293

Query: 306 AEIVNEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVPLLVSKMP 365
            EI    G  +G+V SGGF PTL  P++MGYV +++ A  T +  I+RGK  P  V+ +P
Sbjct: 294 VEITAPDGTPLGTVTSGGFAPTLQAPISMGYVTASHAAPGTEIHVILRGKPQPATVTPLP 353

Query: 366 FVPQRYYR 373
           FVP RY R
Sbjct: 354 FVPHRYKR 361


Lambda     K      H
   0.321    0.138    0.405 

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: 466
Number of extensions: 21
Number of successful extensions: 5
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: 361
Length adjustment: 30
Effective length of query: 344
Effective length of database: 331
Effective search space:   113864
Effective search space used:   113864
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 3609296 Dshi_2682 (glycine cleavage system T protein (RefSeq))
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.27835.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
      4e-95  304.7   0.0    4.6e-95  304.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609296  Dshi_2682 glycine cleavage syste


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609296  Dshi_2682 glycine cleavage system T protein (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.5   0.0   4.6e-95   4.6e-95       1     361 [.       2     356 ..       2     357 .. 0.94

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 4.6e-95
                         TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqy.kslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaL 76 
                                       lk+tpL+ lh elg+k+v+fa we+Pvqy ++++ eh a r+ a lfDvshm ++e++G++  ++L+rl++  +  L
  lcl|FitnessBrowser__Dino:3609296   2 LKKTPLHPLHLELGAKMVPFAWWEMPVQYpTGIMAEHAACREGAALFDVSHMCQMEITGDDPAAALERLVPGGITSL 78 
                                       69***************************55789******************************************* PP

                         TIGR00528  77 tkGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkakt 153
                                       ++G+a+y+ l    GG+ DDliv+++     +++v na+ a++D   l+  l++  tl  + ++ +l+a+qGP a++
  lcl|FitnessBrowser__Dino:3609296  79 APGQARYTQLTTGAGGIYDDLIVTRDPGG--LYVVANASMADQDVGLLRAGLPDC-TL-RVIEDHALIAVQGPAAAA 151
                                       ************************98887..9*****************999864.44.567788************ PP

                         TIGR00528 154 iledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrl 230
                                       ++  l+ + +e+l+ +    +a   +++  ++r GytGedGfei+++   a  ++++l++  g  P GLgarDtLr+
  lcl|FitnessBrowser__Dino:3609296 152 LVAGLVPA-AEDLRFMQSA-QAAWDGQDLRLSRLGYTGEDGFEISLPATAAEAFARALIAG-GAMPAGLGARDTLRM 225
                                       *9999864.5677655555.566778999*******************************9.*************** PP

                         TIGR00528 231 eagmaLyGqeldeeitPleaglgwvvkker.kksdfiGravleeqkengtekklvGlemlekgiarnelkvlltnge 306
                                       eag++LyGq++d+ ++P eaglg+ + k r ++  f G a +    ++g  ++lvGl+   +   r ++++  ++g 
  lcl|FitnessBrowser__Dino:3609296 226 EAGLPLYGQDIDQGTSPPEAGLGFSIPKRRrAEGGFPGAARILGELADGPARRLVGLRPEGRAPVRAGVEITAPDG- 301
                                       **************************88765999******************************************. PP

                         TIGR00528 307 kevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                       +  G vtsG ++PtL+  i+++yv    +  Gt+++v +r+k  ++ v+  +fv+
  lcl|FitnessBrowser__Dino:3609296 302 TPLGTVTSGGFAPTLQAPISMGYVTASHAAPGTEIHVILRGKPQPATVTPLPFVP 356
                                       *************************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (361 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: 00:00:00.01
# Mc/sec: 11.93
//
[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