Alignments for a candidate for carA in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Clostridium acetobutylicum ATCC 824

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate NP_349252.1 CA_C2645 carbamoyl phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_000008765.1:NP_349252.1
          Length = 351

 Score =  359 bits (921), Expect = e-104
 Identities = 164/351 (46%), Positives = 239/351 (68%), Gaps = 2/351 (0%)

Query: 1   MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60
           MK  + LE+G VF G  FG   +  GE+VFNT MTGYQEIL+DPSY GQI+ +TYPLIGN
Sbjct: 1   MKGIIYLEDGTVFYGTGFGKEGNEFGEIVFNTSMTGYQEILTDPSYAGQIINMTYPLIGN 60

Query: 61  YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120
           YG+N    +S   + KG I+K + E PSN+ S   +D+ LK   + G+ G+DTR +T+ I
Sbjct: 61  YGVNESVNQSKCVYAKGFIVKNIDENPSNYTSEINIDQMLKNMGVVGVFGVDTRSITKKI 120

Query: 121 RTAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFGMK 180
           R+ G +K   ++ +  IE + K ++ + +  + V+ VS K      G G ++ ++DFG+K
Sbjct: 121 RSYGTMKCIISNGELSIEELKKMMDASNIVDDYVNTVSTKEIIHIAGNGNKVAVMDFGIK 180

Query: 181 HGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLGKV 240
           + I+  L +R+CD+ + PY+    E+L + PDGI LSNGPGDPK +PEAIE +K ++GK 
Sbjct: 181 NDIIENLKERQCDITIFPYDTDYNEILNINPDGIFLSNGPGDPKSIPEAIENVKKLIGKR 240

Query: 241 PLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTV--SSISK 298
           P+FGICLGHQ+ ALA G NT K+K+GHRG NH + ++   K  +T+QNHGY V   S+ +
Sbjct: 241 PMFGICLGHQIIALASGGNTYKLKYGHRGGNHGIYDVQRDKAYITAQNHGYAVDEESVLE 300

Query: 299 TELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEM 349
             + +TH  +ND T+EG+KHK++P F+VQ+HPE +PGP D  +LFD+F+ +
Sbjct: 301 NGMIITHRNLNDGTVEGMKHKSIPLFSVQFHPEGAPGPTDTTYLFDQFVNL 351


Lambda     K      H
   0.317    0.136    0.397 

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: 399
Number of extensions: 19
Number of successful extensions: 2
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: 351
Length adjustment: 29
Effective length of query: 335
Effective length of database: 322
Effective search space:   107870
Effective search space used:   107870
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: 49 (23.5 bits)

Align candidate NP_349252.1 CA_C2645 (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.21959.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.8e-156  506.6   3.6     2e-156  506.4   3.6    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349252.1  CA_C2645 carbamoyl phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349252.1  CA_C2645 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.4   3.6    2e-156    2e-156       2     357 ..       4     350 ..       3     351 .] 0.98

  Alignments for each domain:
  == domain 1  score: 506.4 bits;  conditional E-value: 2e-156
                              TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikv 73 
                                            +++ledGtvf g++fg+e++ +Ge+vFnTsmtGYqEiltDpsY+gqi+ +typlignygvne+ ++sk +++
  lcl|NCBI__GCF_000008765.1:NP_349252.1   4 IIYLEDGTVFYGTGFGKEGNEFGEIVFNTSMTGYQEILTDPSYAGQIINMTYPLIGNYGVNESVNQSKCVYA 75 
                                            689********************************************************************* PP

                              TIGR01368  74 kglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakes 145
                                            kg++vk++ +++sny+++ +++++lk++g+v++ gvDTR+++kk+R+ g+mk++is+ + + eel++++++s
  lcl|NCBI__GCF_000008765.1:NP_349252.1  76 KGFIVKNIDENPSNYTSEINIDQMLKNMGVVGVFGVDTRSITKKIRSYGTMKCIISNGELSIEELKKMMDAS 147
                                            **************************************************************9*99999999 PP

                              TIGR01368 146 pkvkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnp 217
                                            + v+  ++v++vstke +++      +g+k  v+v+d+G+K++i+++L++r++++t++p+dt+++ei ++np
  lcl|NCBI__GCF_000008765.1:NP_349252.1 148 NIVD--DYVNTVSTKEIIHIAG----NGNK--VAVMDFGIKNDIIENLKERQCDITIFPYDTDYNEILNINP 211
                                            9887..9***********9994....5666..**************************************** PP

                              TIGR01368 218 dgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrv 289
                                            dgi+lsnGPGdP+++ eaie+vkkl++ k P+fGIclGhq++ala+g++tyklk+GhrG+Nh + d+++++ 
  lcl|NCBI__GCF_000008765.1:NP_349252.1 212 DGIFLSNGPGDPKSIPEAIENVKKLIG-KRPMFGICLGHQIIALASGGNTYKLKYGHRGGNHGIYDVQRDKA 282
                                            ***************************.******************************************** PP

                              TIGR01368 290 eitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefve 357
                                            +it+qNHgyavdees+ e+ + +th+nlnDgtveg++hk++p+fsvQ+HPe++pGp+dt+ylFd+fv+
  lcl|NCBI__GCF_000008765.1:NP_349252.1 283 YITAQNHGYAVDEESVLENGMIITHRNLNDGTVEGMKHKSIPLFSVQFHPEGAPGPTDTTYLFDQFVN 350
                                            ******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (351 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: 7.87
//
[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