Alignments for a candidate for carA in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Haloechinothrix alba DSM 45207

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_089301240.1 CHB84_RS09195 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_900188115.1:WP_089301240.1
          Length = 364

 Score =  303 bits (777), Expect = 4e-87
 Identities = 164/375 (43%), Positives = 217/375 (57%), Gaps = 21/375 (5%)

Query: 8   VLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTND 67
           +LEDG+ F G   GA G A GEVVF T MTGYQE LTDPSY +QIV  T P IGN G ND
Sbjct: 1   MLEDGSVFRGLRYGAAGRAFGEVVFCTGMTGYQETLTDPSYHKQIVVQTAPQIGNTGWND 60

Query: 68  ADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLREKGA 127
            D+ESS++   G  +RD   + SN+R+   L + L+R  +V IA +DTR LTR +RE GA
Sbjct: 61  EDDESSRIWVAGYAVRDPARVPSNWRSARSLETELERQGVVGIAQLDTRTLTRHIREHGA 120

Query: 128 QNGCIIAGDNPDAA-LALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEAKK 186
               + +G     A   L +    P + G DLA EVTTAE Y                + 
Sbjct: 121 MRAGVFSGTEVGTAEQMLARVTESPSMTGADLAGEVTTAEPY--------------VVRP 166

Query: 187 EDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGDPA 246
           +  + + V A D G K N  RM+  RG  + ++PA  S ++VL + P G+FLSNGPGDPA
Sbjct: 167 DGPVRYRVAAVDMGIKSNTPRMMAQRGIEVHVLPATASLDEVLAVEPHGVFLSNGPGDPA 226

Query: 247 PCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNVVM 306
              +     +  L+  +P+FGIC G+Q+L  A G  T KM++GH G N PV D     + 
Sbjct: 227 TTTHVTELTRNVLQRQVPLFGICFGNQILGRALGLGTYKMRYGHRGMNIPVMDTATRRIA 286

Query: 307 ITAQNHGFAVDE------ATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           ITAQNHGFA++       ++      ++H    DGT++G+   D PAFS Q HPEA+ GP
Sbjct: 287 ITAQNHGFALEGEPGARFSSPYGAATISHHCPNDGTVEGVRCLDVPAFSVQYHPEAAAGP 346

Query: 361 HDAAPLFDHFIELIE 375
           HDAA LFD F+ L+E
Sbjct: 347 HDAAVLFDEFVSLME 361


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: 390
Number of extensions: 9
Number of successful extensions: 4
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: 364
Length adjustment: 30
Effective length of query: 352
Effective length of database: 334
Effective search space:   117568
Effective search space used:   117568
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 WP_089301240.1 CHB84_RS09195 (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.21554.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-135  437.3   0.0   2.2e-135  437.2   0.0    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089301240.1  CHB84_RS09195 carbamoyl-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089301240.1  CHB84_RS09195 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.2   0.0  2.2e-135  2.2e-135       4     360 ..       1     361 [.       1     362 [. 0.96

  Alignments for each domain:
  == domain 1  score: 437.2 bits;  conditional E-value: 2.2e-135
                                 TIGR01368   4 vledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkik 72 
                                               +ledG+vf+g  +ga + ++GevvF+T+mtGYqE+ltDpsY++qivv t+p+ign+g+n+ed es++i+
  lcl|NCBI__GCF_900188115.1:WP_089301240.1   1 MLEDGSVFRGLRYGAAGRAFGEVVFCTGMTGYQETLTDPSYHKQIVVQTAPQIGNTGWNDEDDESSRIW 69 
                                               59******************************************************************* PP

                                 TIGR01368  73 vkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse..keelv 139
                                               v+g  v++ ++ +sn+r+ +sLe+ l+++g+v+i+++DTR+l++++Re+g+m+a + + ++   +e+  
  lcl|NCBI__GCF_900188115.1:WP_089301240.1  70 VAGYAVRDPARVPSNWRSARSLETELERQGVVGIAQLDTRTLTRHIREHGAMRAGVFSGTEVgtAEQML 138
                                               ******************************************************999877545589999 PP

                                 TIGR01368 140 ekakespkvkevnlvkevstkeayeleqkakkegkk.lrvvvidlGvKenilreLvkrgvevtvvpadt 207
                                               ++++esp++++++l+ ev+t+e+y ++     +g   +rv+++d+G+K+n+ r++++rg+ev+v+pa++
  lcl|NCBI__GCF_900188115.1:WP_089301240.1 139 ARVTESPSMTGADLAGEVTTAEPYVVRP----DGPVrYRVAAVDMGIKSNTPRMMAQRGIEVHVLPATA 203
                                               9***********************9996....455459******************************* PP

                                 TIGR01368 208 saeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrG 276
                                               s++e+ +++p+g++lsnGPGdPa+ +++ e ++++l++++P+fGIc+G+q+l++alg  tyk+++GhrG
  lcl|NCBI__GCF_900188115.1:WP_089301240.1 204 SLDEVLAVEPHGVFLSNGPGDPATTTHVTELTRNVLQRQVPLFGICFGNQILGRALGLGTYKMRYGHRG 272
                                               ********************************************************************* PP

                                 TIGR01368 277 aNhpvkdlktgrveitsqNHgyavdees.....lkeeelevthvnlnDgtveglehkelpvfsvQyHPe 340
                                               +N+pv+d++t r+ it+qNHg+a++ e       + +++++ h++ nDgtveg++  ++p+fsvQyHPe
  lcl|NCBI__GCF_900188115.1:WP_089301240.1 273 MNIPVMDTATRRIAITAQNHGFALEGEPgarfsSPYGAATISHHCPNDGTVEGVRCLDVPAFSVQYHPE 341
                                               ************************988544444678999****************************** PP

                                 TIGR01368 341 aspGphdteylFdefvelik 360
                                               a++Gphd+++lFdefv+l++
  lcl|NCBI__GCF_900188115.1:WP_089301240.1 342 AAAGPHDAAVLFDEFVSLME 361
                                               ****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (364 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.36
//
[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