Alignments for a candidate for gcvT in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Synechococcus elongatus PCC 7942

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate Synpcc7942_2308 Synpcc7942_2308 glycine cleavage system aminomethyltransferase T

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__SynE:Synpcc7942_2308
          Length = 372

 Score =  251 bits (640), Expect = 3e-71
 Identities = 150/366 (40%), Positives = 208/366 (56%), Gaps = 16/366 (4%)

Query: 5   TPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTRE 64
           +PL+   T  GAR   F GW +PL +   + EH AVR  AG+FD+SHM    LRGS  R 
Sbjct: 12  SPLHSVCTSAGARFTGFAGWELPLQFQGLMQEHLAVRERAGLFDISHMGKFQLRGSGLRA 71

Query: 65  FLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYF-----TEDFFRLVVNSATRE 119
            L+ LL +D+  L   G+A YS +LN +GG +DDLIVY+       E  F L+VN+AT +
Sbjct: 72  ALQRLLPSDLTTLLP-GQAQYSVLLNEAGGCLDDLIVYWQGIVDGVEQAF-LIVNAATTD 129

Query: 120 KDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQA 179
            D  W+T+H  P    + +  DL+++A+QGP A A    L +    +          +  
Sbjct: 130 SDRLWLTEHLPPAIALLDLSQDLALVAIQGPQAIAFLQPLVSCDLAELPRFSHTVTSIAG 189

Query: 180 GDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQE 239
              F+A TGYTGE G E+ LP   A   W+ L  AGV PCGLGARDTLRLEA M LYG E
Sbjct: 190 QPAFVARTGYTGEDGCEVMLPPAAAITLWQQLTAAGVVPCGLGARDTLRLEAAMPLYGHE 249

Query: 240 MDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTE-KLVGLVMTEKGVLRNELPV 298
           +D   +PL A +GW +  +  + DF+GR+ L   + +G E +LVGL +  + + R+  PV
Sbjct: 250 LDTDTNPLEAGLGWVVHLD-RNPDFLGRDRLVQAKTNGLERRLVGLELPGRNIARHGYPV 308

Query: 299 RFTDAQGNQHEGIITSGTFSPTLGYSIALARVP---EGIGETAIVQIRNREMPVKVTKPV 355
              D       GI+TSG++SPTL  +IALA VP     +G+   V+IR +++P  V K  
Sbjct: 309 AIADTT----VGIVTSGSWSPTLSKAIALAYVPPALANLGQELWVEIRGKQVPATVVKRP 364

Query: 356 FVRNGK 361
           F R  +
Sbjct: 365 FYRGSQ 370


Lambda     K      H
   0.320    0.136    0.402 

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: 379
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: 364
Length of database: 372
Length adjustment: 30
Effective length of query: 334
Effective length of database: 342
Effective search space:   114228
Effective search space used:   114228
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 Synpcc7942_2308 Synpcc7942_2308 (glycine cleavage system aminomethyltransferase T)
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.12304.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-135  436.9   0.0     3e-135  436.7   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2308  Synpcc7942_2308 glycine cleavage


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2308  Synpcc7942_2308 glycine cleavage system aminomethyltransferase T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.7   0.0    3e-135    3e-135       3     361 ..      11     367 ..       9     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.7 bits;  conditional E-value: 3e-135
                                 TIGR00528   3 rtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllan 71 
                                                 pL+   t+ g++ + faGwelP+q+++l++eh avr+ aGlfD+shmgk++l+Gs  +++Lqrll++
  lcl|FitnessBrowser__SynE:Synpcc7942_2308  11 SSPLHSVCTSAGARFTGFAGWELPLQFQGLMQEHLAVRERAGLFDISHMGKFQLRGSGLRAALQRLLPS 79 
                                               579****************************************************************** PP

                                 TIGR00528  72 DvdaLtkGkaqysvllnaqGGvvDDlivykeged...nrfllvvnaataekDlewlkehleeevtldtl 137
                                               D+  L +G+aqysvlln  GG +DDlivy +g     ++  l+vnaat++ D+ wl+ehl++ + l +l
  lcl|FitnessBrowser__SynE:Synpcc7942_2308  80 DLTTLLPGQAQYSVLLNEAGGCLDDLIVYWQGIVdgvEQAFLIVNAATTDSDRLWLTEHLPPAIALLDL 148
                                               *****************************998543455889**************************** PP

                                 TIGR00528 138 skeisllalqGPkaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekave 206
                                               s++++l+a+qGP+a + l++l++ ++ +l+ f +   + +a++ a++artGytGedG e+++++  a+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_2308 149 SQDLALVAIQGPQAIAFLQPLVSCDLAELPRFSHT-VTSIAGQPAFVARTGYTGEDGCEVMLPPAAAIT 216
                                               **********************************9.899****************************** PP

                                 TIGR00528 207 lwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqk 275
                                               lw++l +a gv P+GLgarDtLrlea m+LyG+eld ++ Pleaglgwvv+++ ++ df+Gr+ l + k
  lcl|FitnessBrowser__SynE:Synpcc7942_2308 217 LWQQLTAA-GVVPCGLGARDTLRLEAAMPLYGHELDTDTNPLEAGLGWVVHLD-RNPDFLGRDRLVQAK 283
                                               ********.********************************************.89************* PP

                                 TIGR00528 276 engtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtkleve 344
                                                ng e++lvGle+  ++iar++++v    ++++vGivtsG+ sPtL k+ialayv+  l++ G++l ve
  lcl|FitnessBrowser__SynE:Synpcc7942_2308 284 TNGLERRLVGLELPGRNIARHGYPVAI--ADTTVGIVTSGSWSPTLSKAIALAYVPPALANLGQELWVE 350
                                               ***************************..667************************************* PP

                                 TIGR00528 345 vrnklvkikvvkklfvr 361
                                               +r+k+v++ vvk++f+r
  lcl|FitnessBrowser__SynE:Synpcc7942_2308 351 IRGKQVPATVVKRPFYR 367
                                               ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (372 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: 8.02
//
[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