Alignments for a candidate for carA in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Haloglycomyces albus DSM 45210

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate WP_025274770.1 HALAL_RS0114940 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>NCBI__GCF_000527155.1:WP_025274770.1
          Length = 394

 Score =  278 bits (712), Expect = 2e-79
 Identities = 160/394 (40%), Positives = 224/394 (56%), Gaps = 36/394 (9%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A LVLEDG  +  +++GA G    E VFNT++TGYQE LTDPSY GQ V+ T PQIGNTG
Sbjct: 7   AILVLEDGRTFHGEAYGAVGETFGEGVFNTAMTGYQETLTDPSYHGQVVVQTAPQIGNTG 66

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           +N +D+ES    + G VI + S   SNWR T+ L D L ++ ++G+  +DTRA+TR LRE
Sbjct: 67  INDEDDESDHIRVAGYVINDPSHIRSNWRSTRGLEDTLAQQGVVGICGVDTRALTRHLRE 126

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSWDIVGIDLISDVSCKSPYEWVDKTNAEWDFNTNSR 237
            G++   +S+E +       ++  S  + G +L            VD+   E  +     
Sbjct: 127 HGAMRVGISSESTDVAALAERVRHSPGMEGANL------------VDRVTTEEKYVVGPD 174

Query: 238 DGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGPGDPSA 297
           +   Y V A D GIK+N  RRL+  G +  V P+     E L + PD +  SNGPGDP+ 
Sbjct: 175 EPPRYTVAALDLGIKRNTPRRLAERGVETHVFPAHTGVDELLSVEPDAVFLSNGPGDPAT 234

Query: 298 VPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRTGQVEI 356
               V T  ELL + VPV+GIC G+Q+LG+ALG +TFK+ +GH G N PV +  T +VE+
Sbjct: 235 AEVQVATTVELLRRGVPVFGICFGNQILGRALGLETFKLAYGHRGINQPVLDRHTEKVEV 294

Query: 357 SAQNHNYAV---DPASLPGG--------------------VEVTHVNLNDGSCAGLSFPE 393
           +A NH +A+   D A+  GG                    VEV+HV LND    GL+  +
Sbjct: 295 TAHNHGFALRMPDAAATDGGEFDPTAHLGPTPTFQTEFGEVEVSHVCLNDNVVEGLTCRD 354

Query: 394 MNVMSLQYHPEASPGPHDSDNAFREFIELMKRSK 427
           +   S+QYHPEA+ GPHD+D  F   ++L+   K
Sbjct: 355 VPAFSVQYHPEAAAGPHDADYLFDRLVQLIDTHK 388


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: 491
Number of extensions: 18
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: 430
Length of database: 394
Length adjustment: 31
Effective length of query: 399
Effective length of database: 363
Effective search space:   144837
Effective search space used:   144837
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_025274770.1 HALAL_RS0114940 (glutamine-hydrolyzing 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.931435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-134  433.9   0.0   1.3e-133  431.4   0.0    1.8  1  NCBI__GCF_000527155.1:WP_025274770.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000527155.1:WP_025274770.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.4   0.0  1.3e-133  1.3e-133       1     360 [.       7     385 ..       7     386 .. 0.97

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 1.3e-133
                             TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikv 73 
                                           a+lvledG++f+g+++ga +e++Ge vFnT+mtGYqE+ltDpsY+gq+vv t+p+ign+g+n+ed es++i v
  NCBI__GCF_000527155.1:WP_025274770.1   7 AILVLEDGRTFHGEAYGAVGETFGEGVFNTAMTGYQETLTDPSYHGQVVVQTAPQIGNTGINDEDDESDHIRV 79 
                                           68*********************************************************************** PP

                             TIGR01368  74 kglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakesp 146
                                           +g v+++ s+  sn+r+++ Le+ l+++g+v+i gvDTRal+++lRe+g+m+  is+e+++   l+e++++sp
  NCBI__GCF_000527155.1:WP_025274770.1  80 AGYVINDPSHIRSNWRSTRGLEDTLAQQGVVGICGVDTRALTRHLREHGAMRVGISSESTDVAALAERVRHSP 152
                                           ************************************************************************* PP

                             TIGR01368 147 kvkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdg 219
                                            ++++nlv++v+t+e+y +      e  +++v+++dlG+K+n+ r+L++rgve++v+pa+t ++e+ +++pd+
  NCBI__GCF_000527155.1:WP_025274770.1 153 GMEGANLVDRVTTEEKYVVGP---DEPPRYTVAALDLGIKRNTPRRLAERGVETHVFPAHTGVDELLSVEPDA 222
                                           *****************9996...4566699****************************************** PP

                             TIGR01368 220 illsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveit 292
                                           ++lsnGPGdPa++e +++t+ +ll + +P+fGIc+G+q+l++alg +t+kl +GhrG N+pv d +t++ve+t
  NCBI__GCF_000527155.1:WP_025274770.1 223 VFLSNGPGDPATAEVQVATTVELLRRGVPVFGICFGNQILGRALGLETFKLAYGHRGINQPVLDRHTEKVEVT 295
                                           ************************************************************************* PP

                             TIGR01368 293 sqNHgyavdees......................lkeeelevthvnlnDgtveglehkelpvfsvQyHPeasp 343
                                           ++NHg+a+                          ++ +e+ev hv+lnD+ vegl+ +++p+fsvQyHPea++
  NCBI__GCF_000527155.1:WP_025274770.1 296 AHNHGFALRMPDaaatdggefdptahlgptptfqTEFGEVEVSHVCLNDNVVEGLTCRDVPAFSVQYHPEAAA 368
                                           *******975434678999**********999888899*********************************** PP

                             TIGR01368 344 GphdteylFdefvelik 360
                                           Gphd++ylFd++v+li+
  NCBI__GCF_000527155.1:WP_025274770.1 369 GPHDADYLFDRLVQLID 385
                                           *************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (394 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.28
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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