Alignments for a candidate for carA in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Desulfatiglans anilini DSM 4660

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate WP_028321758.1 H567_RS0113165 carbamoyl-phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>NCBI__GCF_000422285.1:WP_028321758.1
          Length = 383

 Score =  359 bits (922), Expect = e-104
 Identities = 179/376 (47%), Positives = 251/376 (66%), Gaps = 7/376 (1%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L LEDG+++P +SF  P   + E+VFNTS++GYQE+LTDPSY GQ V MT P +GN G
Sbjct: 3   ALLALEDGTLFPGRSFTGPAEAVGEVVFNTSMSGYQEVLTDPSYCGQMVTMTYPLMGNYG 62

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           VN +D ES +  +   ++R      SNWR   +LA+YLT   I G+  +DTRA+TR LR 
Sbjct: 63  VNDEDVESDRIQVRAFLVREYQEYPSNWRSKGSLAEYLTAAGIPGLEGIDTRALTRHLRV 122

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSWDIVGIDLISDVSCKSPYEWVDKTNAEWD-----F 232
            G++ G LST        + +  ++ D++G+DL+ +V+C+ P  W +   +  +     F
Sbjct: 123 SGAMRGALSTRDLDPHSLVEKARQAPDMLGLDLVREVTCRRPMLWTEGNPSPIEGGLEGF 182

Query: 233 NTNSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGP 292
               R G +++V+A DFG+K NILR L+  GC I +VP+  P A   +++PDG+  SNGP
Sbjct: 183 RWPERPG-AWRVVAMDFGVKYNILRSLAQRGCTILMVPADTPGALIDRLDPDGLFLSNGP 241

Query: 293 GDPSAVPYAVETVKELLGKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRTG 352
           GDP+AV Y + ++++ LGK P++GIC+GHQL+G ALGG +FK+KFGH GGN PV++  TG
Sbjct: 242 GDPAAVTYGIASIRDQLGKRPIFGICLGHQLIGLALGGTSFKLKFGHRGGNQPVQDLTTG 301

Query: 353 QVEISAQNHNYAVDPASL-PGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHD 411
           +VEI++QNH + VD  SL    VEVTHVNLNDG+  GL    + + S+QYHPEASPGPHD
Sbjct: 302 KVEITSQNHGFCVDMGSLAEKDVEVTHVNLNDGTLEGLVHKRIPLFSVQYHPEASPGPHD 361

Query: 412 SDNAFREFIELMKRSK 427
           +   F  FI LMKR +
Sbjct: 362 AAYLFDRFIALMKRHR 377


Lambda     K      H
   0.316    0.134    0.403 

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: 492
Number of extensions: 16
Number of successful extensions: 3
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: 430
Length of database: 383
Length adjustment: 31
Effective length of query: 399
Effective length of database: 352
Effective search space:   140448
Effective search space used:   140448
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_028321758.1 H567_RS0113165 (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.26374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-153  497.5   0.0   1.2e-153  497.3   0.0    1.0  1  lcl|NCBI__GCF_000422285.1:WP_028321758.1  H567_RS0113165 carbamoyl-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000422285.1:WP_028321758.1  H567_RS0113165 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.3   0.0  1.2e-153  1.2e-153       1     360 [.       3     374 ..       3     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 497.3 bits;  conditional E-value: 1.2e-153
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a l+ledGt f g+sf  + e+vGevvFnTsm+GYqE+ltDpsY gq+v++typl+gnygvn+ed+es+
  lcl|NCBI__GCF_000422285.1:WP_028321758.1   3 ALLALEDGTLFPGRSFTGPAEAVGEVVFNTSMSGYQEVLTDPSYCGQMVTMTYPLMGNYGVNDEDVESD 71 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138
                                               +i+v++++v+e+++ +sn+r+k sL+e+l+  gi+++eg+DTRal+++lR +g+m++++st++ + ++l
  lcl|NCBI__GCF_000422285.1:WP_028321758.1  72 RIQVRAFLVREYQEYPSNWRSKGSLAEYLTAAGIPGLEGIDTRALTRHLRVSGAMRGALSTRDLDPHSL 140
                                               ********************************************************************* PP

                                 TIGR01368 139 vekakespkvkevnlvkevstkeayeleq..........k....akkegkklrvvvidlGvKenilreL 193
                                               veka+++p++ +++lv+ev++++++ +++          +     ++ g   rvv++d+GvK nilr+L
  lcl|NCBI__GCF_000422285.1:WP_028321758.1 141 VEKARQAPDMLGLDLVREVTCRRPMLWTEgnpspiegglEgfrwPERPGA-WRVVAMDFGVKYNILRSL 208
                                               ****************************9887777665516543344444.69**************** PP

                                 TIGR01368 194 vkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllala 262
                                               ++rg+++ +vpadt+ + i +l+pdg++lsnGPGdPaav++ i+ ++  l+ k PifGIclGhql++la
  lcl|NCBI__GCF_000422285.1:WP_028321758.1 209 AQRGCTILMVPADTPGALIDRLDPDGLFLSNGPGDPAAVTYGIASIRDQLG-KRPIFGICLGHQLIGLA 276
                                               ***************************************************.***************** PP

                                 TIGR01368 263 lgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelp 331
                                               lg+  +klkfGhrG+N+pv+dl+tg+veitsqNHg+ vd  sl e+++evthvnlnDgt+egl hk++p
  lcl|NCBI__GCF_000422285.1:WP_028321758.1 277 LGGTSFKLKFGHRGGNQPVQDLTTGKVEITSQNHGFCVDMGSLAEKDVEVTHVNLNDGTLEGLVHKRIP 345
                                               ********************************************************************* PP

                                 TIGR01368 332 vfsvQyHPeaspGphdteylFdefvelik 360
                                               +fsvQyHPeaspGphd++ylFd+f+ l+k
  lcl|NCBI__GCF_000422285.1:WP_028321758.1 346 LFSVQYHPEASPGPHDAAYLFDRFIALMK 374
                                               **************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (383 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: 10.81
//
[ok]

This GapMind analysis is from Apr 10 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