Alignments for a candidate for carA in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Ammonifex degensii KC4

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_015738404.1 ADEG_RS01865 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_000024605.1:WP_015738404.1
          Length = 359

 Score =  397 bits (1019), Expect = e-115
 Identities = 189/354 (53%), Positives = 260/354 (73%), Gaps = 3/354 (0%)

Query: 1   MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60
           M+  L LE+G VF G AFG+     GEVVF T MTGYQE+L+DPSYCGQIV LTYPL GN
Sbjct: 1   MRALLALEDGTVFSGRAFGARGEVWGEVVFATAMTGYQEVLTDPSYCGQIVVLTYPLAGN 60

Query: 61  YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120
           YGIN +D E+   +V+GL+++E C  PSNWRS  TL E+L+   +PG++G+DTR LTR +
Sbjct: 61  YGINLEDNEAGRVWVRGLVVREYCPTPSNWRSTCTLAEFLQTHGVPGIEGVDTRALTRRL 120

Query: 121 RTAGALKGTFASSDEDIEAVLK--RLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFG 178
           R  G+++G  ++ D D E+++   RL  +    + VS+V  ++AY  PG G R+V+VDFG
Sbjct: 121 REHGSMRGVISTEDLDPESLVAKARLAPSLSEEDLVSEVVTRSAYTIPGEGPRVVVVDFG 180

Query: 179 MKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLG 238
           +K  ILR+L +R C+++VVP   +A+E+L L P G++LSNGPGDP  +  A + +K +LG
Sbjct: 181 VKQSILRQLRERGCELVVVPPTSSAQEILALAPQGVLLSNGPGDPSRLTGARDTVKALLG 240

Query: 239 KVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTVSSIS- 297
           +VPL GICLGHQ+ AL+ GA T K+KFGH G NHPVK+LATG+V +TS NHG+ V   S 
Sbjct: 241 RVPLMGICLGHQVAALSLGARTFKLKFGHHGINHPVKDLATGRVFITSHNHGFAVDPASL 300

Query: 298 KTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMIE 351
             ELEV++I++ND T+EGL+HK LP F+VQ+HPE  PGP+DA  +FDRF+E+++
Sbjct: 301 PPELEVSYISLNDGTVEGLRHKFLPFFSVQFHPEGGPGPQDAAFIFDRFLELLQ 354


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: 414
Number of extensions: 12
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: 364
Length of database: 359
Length adjustment: 29
Effective length of query: 335
Effective length of database: 330
Effective search space:   110550
Effective search space used:   110550
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 WP_015738404.1 ADEG_RS01865 (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.25163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-152  493.2   0.0   2.4e-152  493.0   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015738404.1  ADEG_RS01865 carbamoyl-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738404.1  ADEG_RS01865 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.0   0.0  2.4e-152  2.4e-152       1     360 [.       3     354 ..       3     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 493.0 bits;  conditional E-value: 2.4e-152
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a l+ledGtvf+g++fga++ev GevvF+T+mtGYqE+ltDpsY gqivvltypl gnyg+n ed+e+ 
  lcl|NCBI__GCF_000024605.1:WP_015738404.1   3 ALLALEDGTVFSGRAFGARGEVWGEVVFATAMTGYQEVLTDPSYCGQIVVLTYPLAGNYGINLEDNEAG 71 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138
                                               +++v+glvv+e++ ++sn+r++ +L+efl+++g+++iegvDTRal+++lRe+gsm++viste+ + e+l
  lcl|NCBI__GCF_000024605.1:WP_015738404.1  72 RVWVRGLVVREYCPTPSNWRSTCTLAEFLQTHGVPGIEGVDTRALTRRLREHGSMRGVISTEDLDPESL 140
                                               ********************************************************************* PP

                                 TIGR01368 139 vekakespkvkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadt 207
                                               v+ka+ +p+++e +lv+ev+t++ay++      eg   rvvv+d+GvK++ilr+L +rg+e++vvp ++
  lcl|NCBI__GCF_000024605.1:WP_015738404.1 141 VAKARLAPSLSEEDLVSEVVTRSAYTIPG----EGP--RVVVVDFGVKQSILRQLRERGCELVVVPPTS 203
                                               **************************994....455..5****************************** PP

                                 TIGR01368 208 saeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrG 276
                                               sa+ei +l p+g+llsnGPGdP++++ a +tvk+ll+ ++P++GIclGhq+ al+lga+t+klkfGh+G
  lcl|NCBI__GCF_000024605.1:WP_015738404.1 204 SAQEILALAPQGVLLSNGPGDPSRLTGARDTVKALLG-RVPLMGICLGHQVAALSLGARTFKLKFGHHG 271
                                               *************************************.******************************* PP

                                 TIGR01368 277 aNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGp 345
                                                Nhpvkdl+tgrv+its+NHg+avd++sl+ e lev   +lnDgtvegl+hk lp+fsvQ+HPe+ pGp
  lcl|NCBI__GCF_000024605.1:WP_015738404.1 272 INHPVKDLATGRVFITSHNHGFAVDPASLPPE-LEVSYISLNDGTVEGLRHKFLPFFSVQFHPEGGPGP 339
                                               ****************************9866.************************************ PP

                                 TIGR01368 346 hdteylFdefvelik 360
                                               +d++++Fd+f+el++
  lcl|NCBI__GCF_000024605.1:WP_015738404.1 340 QDAAFIFDRFLELLQ 354
                                               ***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (359 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.74
//
[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