Alignments for a candidate for gcvT in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Cupriavidus basilensis 4G11

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate RR42_RS20060 RR42_RS20060 glycine cleavage system protein T

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__Cup4G11:RR42_RS20060
          Length = 379

 Score =  333 bits (853), Expect = 6e-96
 Identities = 198/384 (51%), Positives = 241/384 (62%), Gaps = 33/384 (8%)

Query: 3   QQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRT 62
           Q TPL   H    ARMVDF GW MP++YGSQI+EHHAVRTDAGMFDVSHM +VDL G   
Sbjct: 4   QATPLNAIHRALSARMVDFGGWDMPVNYGSQIEEHHAVRTDAGMFDVSHMCVVDLNGEHV 63

Query: 63  REFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDL 122
           R FLR LLAN+V KL   GKALYS ML+  GGVIDDLIVY+F ED FRLVVN+ T   D+
Sbjct: 64  RAFLRGLLANNVDKLQTPGKALYSCMLDEKGGVIDDLIVYFFAEDHFRLVVNAGTANNDI 123

Query: 123 SWITQH--AEPFGIEITVR---------DDLSMIAVQGPNAQAKAATLFNDAQRQAVEGM 171
            WI     A   G+ IT R           L+++AVQGPNA+AK    F   Q    E +
Sbjct: 124 EWIAARNAATNSGVRITPRRGDNAPDGVAPLAIVAVQGPNARAKVWNAFPSTQPS--EAL 181

Query: 172 KPFFGV-----QAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDT 226
           KPF  V       G++ +A TGYTGE G+E+ +P E  A  W  L+  GV+P GLGARDT
Sbjct: 182 KPFNAVVVQDPALGEVMVARTGYTGEDGFELVVPAENVAGLWEKLIAEGVRPAGLGARDT 241

Query: 227 LRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVM 286
           LRLEAGMNLYGQ+MD   SPL A + WT+  + ++RDF G+ AL    +  T++ VGL++
Sbjct: 242 LRLEAGMNLYGQDMDIHTSPLNAGLAWTVDLQ-SERDFTGKAALVAGGK--TQQFVGLIL 298

Query: 287 TEK-----GVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVP--EGIGETAI 339
                   GVLR    V  T A     EG ITSGTFSP+L  SIA AR+P    +G    
Sbjct: 299 RPANGKAGGVLRAHQKV-ITPA----GEGEITSGTFSPSLSQSIAFARLPLDVALGAEVQ 353

Query: 340 VQIRNREMPVKVTKPVFVRNGKAV 363
           V+IR+R++   V K  FVRNGKA+
Sbjct: 354 VEIRDRKLAATVVKLPFVRNGKAL 377


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: 437
Number of extensions: 24
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: 379
Length adjustment: 30
Effective length of query: 334
Effective length of database: 349
Effective search space:   116566
Effective search space used:   116566
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 RR42_RS20060 RR42_RS20060 (glycine cleavage system protein 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.7028.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-115  372.1   0.0   1.6e-115  371.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS20060  RR42_RS20060 glycine cleavage sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS20060  RR42_RS20060 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.9   0.0  1.6e-115  1.6e-115       1     362 []       3     373 ..       3     373 .. 0.89

  Alignments for each domain:
  == domain 1  score: 371.9 bits;  conditional E-value: 1.6e-115
                                 TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrll 69 
                                               l+ tpL  +h  l++++vdf+Gw +Pv+y+s+ieeh+avrt+aG+fDvshm  v+l+G+++++fL+ ll
  lcl|FitnessBrowser__Cup4G11:RR42_RS20060   3 LQATPLNAIHRALSARMVDFGGWDMPVNYGSQIEEHHAVRTDAGMFDVSHMCVVDLNGEHVRAFLRGLL 71 
                                               578****************************************************************** PP

                                 TIGR00528  70 anDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkeh..leee.vtl 134
                                               an+vd+L + Gka+ys +l  +GGv+DDlivy ++ed +f+lvvna+ta+ D ew+  +  ++++ v +
  lcl|FitnessBrowser__Cup4G11:RR42_RS20060  72 ANNVDKLQTpGKALYSCMLDEKGGVIDDLIVYFFAED-HFRLVVNAGTANNDIEWIAARnaATNSgVRI 139
                                               *******655***************************.******************7641133331333 PP

                                 TIGR00528 135 dtlskei........sllalqGPkaktiledll.d.kaveglkefffvqeaelalkkaliartGytGed 193
                                                  + +         +++a+qGP+a++ + ++  + +  e+lk+f  v  ++ al + ++artGytGed
  lcl|FitnessBrowser__Cup4G11:RR42_RS20060 140 TPRRGDNapdgvaplAIVAVQGPNARAKVWNAFpStQPSEALKPFNAVVVQDPALGEVMVARTGYTGED 208
                                               3333333577778889*******998755555414144556**************************** PP

                                 TIGR00528 194 GfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkk 262
                                               Gfe++v+ e+ + lw+kl+++ gv+P GLgarDtLrleagm+LyGq++d +++Pl+agl w+v ++ ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS20060 209 GFELVVPAENVAGLWEKLIAE-GVRPAGLGARDTLRLEAGMNLYGQDMDIHTSPLNAGLAWTVDLQ-SE 275
                                               *********************.********************************************.** PP

                                 TIGR00528 263 sdfiGravleeqkengtekklvGleml.....ekgiarnelkvlltngekevGivtsGtlsPtLgknia 326
                                               +df G+a+l      g  ++ vGl +      + g++r + kv+++ g   +G +tsGt+sP L ++ia
  lcl|FitnessBrowser__Cup4G11:RR42_RS20060 276 RDFTGKAALVA---GGKTQQFVGLILRpangkAGGVLRAHQKVITPAG---EGEITSGTFSPSLSQSIA 338
                                               *********85...455566999976422221345**********999...9***************** PP

                                 TIGR00528 327 layvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                                a+++ ++   G +++ve+r++++ + vvk +fvr+
  lcl|FitnessBrowser__Cup4G11:RR42_RS20060 339 FARLPLDV-ALGAEVQVEIRDRKLAATVVKLPFVRN 373
                                               *****776.69***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (379 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.77
//
[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