Alignments for a candidate for gcvT in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Sphingomonas koreensis DSMZ 15582

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate Ga0059261_3256 Ga0059261_3256 glycine cleavage system T protein

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



>FitnessBrowser__Korea:Ga0059261_3256
          Length = 389

 Score =  340 bits (872), Expect = 4e-98
 Identities = 193/378 (51%), Positives = 245/378 (64%), Gaps = 13/378 (3%)

Query: 4   EQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRLT 63
           E+L   PL A H   G RMVPFAGY+MPVQY  G+M EH   R+ AGLFDVSHMGQ+ L+
Sbjct: 12  EELALLPLDAWHRAKGGRMVPFAGYEMPVQYE-GIMAEHLWVRESAGLFDVSHMGQLFLS 70

Query: 64  GAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMV--------ANLGNDELFL 115
           G G   ALE L+P D+  + V  Q+Y++   +NGGILDDLM         A+ G   L++
Sbjct: 71  GDGLDAALEALIPADVAGVKVNGQKYSLLLAQNGGILDDLMFTRWDADNGAHPGAAGLYM 130

Query: 116 VVNAACKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQF 175
           VVN ACK  D+AHLR H+  +  I  + E  ALLALQGP AV  L+RL P V  + FM+ 
Sbjct: 131 VVNGACKWDDIAHLREHLPDEIEINHMDE-HALLALQGPKAVDALSRLVPGVEGLIFMRG 189

Query: 176 QRVTLLGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEA 235
            R    G   ++SRSGYTGEDGFEISV A +A  LA AL A+PEV  IGLGARDSLRLEA
Sbjct: 190 GRFDWNGTSLWISRSGYTGEDGFEISVEADKAAALAGALTAQPEVKPIGLGARDSLRLEA 249

Query: 236 GLCLYGHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLL 295
            L LYGHD++TETTPI A+L +A++  RR + A    FPGAE +  +++ G  ++RVGL+
Sbjct: 250 DLPLYGHDLDTETTPIMAALNFAVASKRRREEA---NFPGAERILLEREQGAIQRRVGLI 306

Query: 296 PQERTPVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGK 355
            + R PVREGA ++++ G  +G V SGGF PT+  P+AM Y+ +A   + T V    RGK
Sbjct: 307 VEGRQPVREGALVLDDEGNEVGRVTSGGFAPTVQKPIAMAYVPTAMAEVGTRVTLSQRGK 366

Query: 356 KVPLLVSKMPFVPQRYYR 373
                V  MPFVP  Y R
Sbjct: 367 IHHGEVVPMPFVPHNYVR 384


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: 446
Number of extensions: 18
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: 389
Length adjustment: 30
Effective length of query: 344
Effective length of database: 359
Effective search space:   123496
Effective search space used:   123496
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 Ga0059261_3256 Ga0059261_3256 (glycine cleavage system T protein)
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.11339.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-104  333.1   0.0   1.1e-103  332.8   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3256  Ga0059261_3256 glycine cleavage 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3256  Ga0059261_3256 glycine cleavage system T protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.8   0.0  1.1e-103  1.1e-103       6     361 ..      19     379 ..      15     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 332.8 bits;  conditional E-value: 1.1e-103
                                 TIGR00528   6 LydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvd 74 
                                               L   h   gg++v+faG+e+Pvqy++++ eh +vr++aGlfDvshmg+  lsG+   ++L+ l+++Dv+
  lcl|FitnessBrowser__Korea:Ga0059261_3256  19 LDAWHRAKGGRMVPFAGYEMPVQYEGIMAEHLWVRESAGLFDVSHMGQLFLSGDGLDAALEALIPADVA 87 
                                               66678999************************************************************* PP

                                 TIGR00528  75 aLtkGkaqysvllnaqGGvvDDlivykeged.......nrfllvvnaataekDlewlkehleeevtldt 136
                                                + +   +ys ll  +GG++DDl+ ++   d         +++vvn a++  D ++l+ehl++e++++ 
  lcl|FitnessBrowser__Korea:Ga0059261_3256  88 GVKVNGQKYSLLLAQNGGILDDLMFTRWDADngahpgaAGLYMVVNGACKWDDIAHLREHLPDEIEIN- 155
                                               ****999******************9987775777765579*********************999875. PP

                                 TIGR00528 137 lskeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekav 205
                                                ++e +llalqGPka + l  l+   vegl  +  + + +  +    i+r+GytGedGfei+v+ +ka+
  lcl|FitnessBrowser__Korea:Ga0059261_3256 156 HMDEHALLALQGPKAVDALSRLVP-GVEGLIFM-RGGRFDWNGTSLWISRSGYTGEDGFEISVEADKAA 222
                                               67899***********99988864.46666433.344777777788*********************** PP

                                 TIGR00528 206 elwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkker..kksdfiGravle 272
                                                l+ +l +++ vkPiGLgarD+Lrlea+++LyG++ld e+tP+ a+l+++v+ +r  ++ +f G + + 
  lcl|FitnessBrowser__Korea:Ga0059261_3256 223 ALAGALTAQPEVKPIGLGARDSLRLEADLPLYGHDLDTETTPIMAALNFAVASKRrrEEANFPGAERIL 291
                                               ***************************************************998766899********* PP

                                 TIGR00528 273 eqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtkl 341
                                                 +e+g+ +++vGl +  ++  r++  vl  +g +evG vtsG ++Pt++k ia+ayv++ ++++Gt++
  lcl|FitnessBrowser__Korea:Ga0059261_3256 292 LEREQGAIQRRVGLIVEGRQPVREGALVLDDEG-NEVGRVTSGGFAPTVQKPIAMAYVPTAMAEVGTRV 359
                                               ******************************888.99********************************* PP

                                 TIGR00528 342 evevrnklvkikvvkklfvr 361
                                               +   r+k+ + +vv ++fv+
  lcl|FitnessBrowser__Korea:Ga0059261_3256 360 TLSQRGKIHHGEVVPMPFVP 379
                                               ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (389 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: 7.66
//
[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