Alignments for a candidate for carA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Sinorhizobium meliloti 1021

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate SMc01569 SMc01569 carbamoyl phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Smeli:SMc01569
          Length = 401

 Score =  372 bits (954), Expect = e-107
 Identities = 198/381 (51%), Positives = 248/381 (65%), Gaps = 10/381 (2%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           +ALLVL DGT   G+ IGATG+   EV FNT++TGYQEILTDPSY  QIVT T+PHIGN+
Sbjct: 13  TALLVLADGTVIEGKGIGATGTVQAEVCFNTALTGYQEILTDPSYLGQIVTFTFPHIGNI 72

Query: 64  GTNDADEE----SSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119
           G ND D E    +++  A G++ +      SN+R  + L ++LK   I+ +  IDTR LT
Sbjct: 73  GANDEDIEDLTPAARHGAVGVIFKADITEPSNYRAAKHLDAWLKARGIIGLCGIDTRALT 132

Query: 120 RLLREKGAQNGCIIAGDNP---DAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWT 176
             +RE G  N  +IA D     D      +A+A+ GL G+DLAK  T+ ++Y W +  W 
Sbjct: 133 AWIRENGMPNA-VIAHDPAGVFDVEALKAEAKAWSGLEGLDLAKVATSGQSYRWNEKPWV 191

Query: 177 LTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGI 236
              G      E +  +HVVA D+G KRNILR+     CR+T+VPAQTSAE+VL + PDGI
Sbjct: 192 WNEGY-STLGETDAAYHVVALDYGVKRNILRLFAGLNCRVTVVPAQTSAEEVLALKPDGI 250

Query: 237 FLSNGPGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNH 295
           FLSNGPGDPA   +YA+  IQ  L+TDIPVFGICLGHQ+LALA GA+T KM  GHHG NH
Sbjct: 251 FLSNGPGDPAATGEYAVPVIQDLLKTDIPVFGICLGHQMLALALGARTEKMHQGHHGANH 310

Query: 296 PVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPE 355
           PVKD     V I + NHGFAVD  +LP  +  TH SLFDGT  G+    +P FS Q HPE
Sbjct: 311 PVKDHTTGKVEIVSMNHGFAVDANSLPQGVEQTHISLFDGTNCGLRVDGRPVFSVQHHPE 370

Query: 356 ASPGPHDAAPLFDHFIELIEQ 376
           ASPGP D+  LF  F+ LI +
Sbjct: 371 ASPGPQDSHYLFRRFLNLIRE 391


Lambda     K      H
   0.318    0.135    0.400 

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: 488
Number of extensions: 22
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: 382
Length of database: 401
Length adjustment: 31
Effective length of query: 351
Effective length of database: 370
Effective search space:   129870
Effective search space used:   129870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate SMc01569 SMc01569 (carbamoyl phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

# 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.aa/TIGR01368.hmm
# target sequence database:        /tmp/gapView.32065.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01368  [M=361]
Accession:   TIGR01368
Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.4e-130  420.1   0.0   3.9e-130  419.9   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc01569  SMc01569 carbamoyl phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01569  SMc01569 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.9   0.0  3.9e-130  3.9e-130       1     360 [.      14     390 ..      14     391 .. 0.93

  Alignments for each domain:
  == domain 1  score: 419.9 bits;  conditional E-value: 3.9e-130
                           TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk....ki 71 
                                         a lvl+dGtv+egk++ga+++v +ev+FnT++tGYqEiltDpsY gqiv++t p+ign+g n+ed+e      + 
  lcl|FitnessBrowser__Smeli:SMc01569  14 ALLVLADGTVIEGKGIGATGTVQAEVCFNTALTGYQEILTDPSYLGQIVTFTFPHIGNIGANDEDIEDLtpaaRH 88 
                                         579***************************************************************866222255 PP

                           TIGR01368  72 kvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelvekak 143
                                          + g++ k   +e+snyra + L+++lk +gi+++ g+DTRal+  +Re+g  +avi+++       e l+++ak
  lcl|FitnessBrowser__Smeli:SMc01569  89 GAVGVIFKADITEPSNYRAAKHLDAWLKARGIIGLCGIDTRALTAWIRENGMPNAVIAHDPAGvfdVEALKAEAK 163
                                         678********************************************************9976666889999999 PP

                           TIGR01368 144 espkvkevnlvkevstkeayeleq.....k.....akkegkklrvvvidlGvKenilreLvkrgvevtvvpadts 208
                                         +   +++++l+k ++  + y++++     +       +++  ++vv++d+GvK+nilr ++  +++vtvvpa+ts
  lcl|FitnessBrowser__Smeli:SMc01569 164 AWSGLEGLDLAKVATSGQSYRWNEkpwvwNegystLGETDAAYHVVALDYGVKRNILRLFAGLNCRVTVVPAQTS 238
                                         999********************955555156653444555599******************************* PP

                           TIGR01368 209 aeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvk 282
                                         aee+ +l+pdgi+lsnGPGdPaa  e+a+  ++ ll+++iP+fGIclGhq+lalalga+t k++ Gh+GaNhpvk
  lcl|FitnessBrowser__Smeli:SMc01569 239 AEEVLALKPDGIFLSNGPGDPAATgEYAVPVIQDLLKTDIPVFGICLGHQMLALALGARTEKMHQGHHGANHPVK 313
                                         *********************8763778999******************************************** PP

                           TIGR01368 283 dlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefve 357
                                         d++tg+vei s NHg+avd +sl+++ +e th +l+Dgt+ gl+    pvfsvQ+HPeaspGp+d++ylF++f++
  lcl|FitnessBrowser__Smeli:SMc01569 314 DHTTGKVEIVSMNHGFAVDANSLPQG-VEQTHISLFDGTNCGLRVDGRPVFSVQHHPEASPGPQDSHYLFRRFLN 387
                                         **********************9876.************************************************ PP

                           TIGR01368 358 lik 360
                                         li+
  lcl|FitnessBrowser__Smeli:SMc01569 388 LIR 390
                                         997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (401 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: 12.63
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis