Alignments for a candidate for carA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate Echvi_0226 Echvi_0226 carbamoyl-phosphate synthase, small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Cola:Echvi_0226
          Length = 364

 Score =  296 bits (759), Expect = 5e-85
 Identities = 168/376 (44%), Positives = 220/376 (58%), Gaps = 22/376 (5%)

Query: 3   KSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGN 62
           + A L+LEDGT F+G  IG  G+  GE+ FNT MTGYQEI TDPSY+ QIV  T  HIGN
Sbjct: 4   QKATLLLEDGTVFYGTLIGKHGTNGGEICFNTGMTGYQEIYTDPSYTGQIVVTTTSHIGN 63

Query: 63  VGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLL 122
            G  D++ ES       +V+     I S    T+ L  +L+ + I  IAD+DTRKL R +
Sbjct: 64  YGVIDSEAESDGPTIASIVVNSFSEIYSRLDATQSLQEFLESNGITGIADVDTRKLVRHI 123

Query: 123 REKGAQNGCIIAG-DN-PDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           R KGA N  I +  DN  D    L+K    P + G++L+ +V T E Y     + T+   
Sbjct: 124 RSKGAMNAIISSEFDNLEDLQKELDKV---PDMAGLELSSKVCTKEPYYVGDENSTIK-- 178

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
                        V   D+G KRNILR L  RG    + PA+T+  D+    P+  FLSN
Sbjct: 179 -------------VACVDYGIKRNILRNLAARGVYCKVFPAKTAVADMEAWQPNAYFLSN 225

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDPA  DYA+  +++ L  + PVFGICLGHQLLA A G KT KM  GH G NHP+K++
Sbjct: 226 GPGDPAVMDYAVETVKEILALNKPVFGICLGHQLLAEAVGIKTYKMHHGHRGINHPIKNL 285

Query: 301 EKNVVMITAQNHGFAV--DEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358
                 IT+QNHGF +  +++    ++ +TH  L D T+ GI   D+PAFS Q HPE++P
Sbjct: 286 NTGKSEITSQNHGFNIVREDSENHPDIEITHVHLNDNTVAGIKLKDRPAFSVQYHPESAP 345

Query: 359 GPHDAAPLFDHFIELI 374
           GPHD+  LFD FI LI
Sbjct: 346 GPHDSRYLFDDFISLI 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: 392
Number of extensions: 13
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: 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 Echvi_0226 Echvi_0226 (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.11686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   9.3e-142  458.2   0.2   1.1e-141  458.0   0.2    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0226  Echvi_0226 carbamoyl-phosphate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0226  Echvi_0226 carbamoyl-phosphate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.0   0.2  1.1e-141  1.1e-141       1     360 [.       6     362 ..       6     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 458.0 bits;  conditional E-value: 1.1e-141
                            TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                          atl+ledGtvf g+ +g++++  Ge++FnT+mtGYqEi tDpsY+gqivv t+ +ignygv +++aes+ ++++
  lcl|FitnessBrowser__Cola:Echvi_0226   6 ATLLLEDGTVFYGTLIGKHGTNGGEICFNTGMTGYQEIYTDPSYTGQIVVTTTSHIGNYGVIDSEAESDGPTIA 79 
                                          689*********************************************************************** PP

                            TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkv 148
                                          ++vv+ +s+ +s   a++sL+efl+++gi +i++vDTR+lv+++R+kg+m+a+is+e  + e+l++++++ p++
  lcl|FitnessBrowser__Cola:Echvi_0226  80 SIVVNSFSEIYSRLDATQSLQEFLESNGITGIADVDTRKLVRHIRSKGAMNAIISSEFDNLEDLQKELDKVPDM 153
                                          ************************************************************************** PP

                            TIGR01368 149 kevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgill 222
                                          ++++l ++v+tke+y++ +    e+++ +v+ +d+G+K+nilr+L++rgv  +v+pa+t ++++++ +p++ +l
  lcl|FitnessBrowser__Cola:Echvi_0226 154 AGLELSSKVCTKEPYYVGD----ENSTIKVACVDYGIKRNILRNLAARGVYCKVFPAKTAVADMEAWQPNAYFL 223
                                          ***************9996....566689********************************************* PP

                            TIGR01368 223 snGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNH 296
                                          snGPGdPa +++a+etvk++l  ++P+fGIclGhqlla a+g ktyk++ GhrG Nhp+k+l+tg+ eitsqNH
  lcl|FitnessBrowser__Cola:Echvi_0226 224 SNGPGDPAVMDYAVETVKEILALNKPVFGICLGHQLLAEAVGIKTYKMHHGHRGINHPIKNLNTGKSEITSQNH 297
                                          ************************************************************************** PP

                            TIGR01368 297 gya.vdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                          g++ v e+s ++ ++e+thv+lnD+tv+g++ k+ p+fsvQyHPe++pGphd++ylFd+f++li+
  lcl|FitnessBrowser__Cola:Echvi_0226 298 GFNiVREDSENHPDIEITHVHLNDNTVAGIKLKDRPAFSVQYHPESAPGPHDSRYLFDDFISLIN 362
                                          **83578888999************************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.53
//
[ok]

This GapMind analysis is from Apr 09 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