Alignments for a candidate for carA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Shewanella loihica PV-4

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate 5210398 Shew_2839 carbamoyl phosphate synthase small subunit (RefSeq)

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__PV4:5210398
          Length = 390

 Score =  350 bits (898), Expect = e-101
 Identities = 177/380 (46%), Positives = 237/380 (62%), Gaps = 9/380 (2%)

Query: 57  NARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNT 116
           +A LVLEDG+++   + GA G  + E+VFNTS+TGYQEILTDPSY+ Q V +T P IGNT
Sbjct: 13  SALLVLEDGTVFSGTAIGADGLAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNT 72

Query: 117 GVNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLR 176
           G N +D ES      GL+IR+L +  SN+R  ++L+DYL   +++G+ D+DTR +TR LR
Sbjct: 73  GTNSEDTESEAVHACGLIIRDLPLLASNFRNEQSLSDYLKSNNVVGIADIDTRKLTRILR 132

Query: 177 EDGSLIGVLSTEQSKTDDELLQMSRSWDIVGIDLISDVSCKSPYEWVDKTNAEWDF---- 232
           E G+  G +          L        + G+DL  +V+ +  Y+W    +  W      
Sbjct: 133 EKGAQAGAILVGDMDEAKALAAAKAFPGLKGMDLAKEVTTQKQYQW---RSGSWRLVGGL 189

Query: 233 -NTNSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNG 291
            +        YKV+AYD+G+K+NILR L   GC +TVVP+  PAAE L MNPDGI  SNG
Sbjct: 190 PSDTPESELKYKVVAYDYGVKRNILRMLVDRGCDVTVVPAQTPAAEVLAMNPDGIFLSNG 249

Query: 292 PGDPSAVPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNR 350
           PGDP    YA+E ++  L   +P++GIC+GHQLL  A G KT KMKFGHHG NHPV N  
Sbjct: 250 PGDPEPCDYAIEAIQAFLKTDIPLFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNLE 309

Query: 351 TGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPH 410
            G V I++QNH +A D  SLP  V+VTH +L DGS  G+   +    S Q HPEASPGPH
Sbjct: 310 KGNVMITSQNHGFAADETSLPANVKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGPH 369

Query: 411 DSDNAFREFIELMKRSKQSS 430
           D+   F  FIEL++  + ++
Sbjct: 370 DAAPLFDHFIELIEEYRHNA 389


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: 464
Number of extensions: 16
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: 430
Length of database: 390
Length adjustment: 31
Effective length of query: 399
Effective length of database: 359
Effective search space:   143241
Effective search space used:   143241
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 5210398 Shew_2839 (carbamoyl phosphate synthase small subunit (RefSeq))
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.21792.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.3e-154  500.5   0.0   1.4e-154  500.3   0.0    1.0  1  lcl|FitnessBrowser__PV4:5210398  Shew_2839 carbamoyl phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210398  Shew_2839 carbamoyl phosphate synthase small subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.3   0.0  1.4e-154  1.4e-154       1     360 [.      14     383 ..      14     384 .. 0.97

  Alignments for each domain:
  == domain 1  score: 500.3 bits;  conditional E-value: 1.4e-154
                        TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvv 78 
                                      a lvledGtvf+g+++ga++ +vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ed+es+ +++ gl++
  lcl|FitnessBrowser__PV4:5210398  14 ALLVLEDGTVFSGTAIGADGLAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNTGTNSEDTESEAVHACGLII 91 
                                      579*************************************************************************** PP

                        TIGR01368  79 kelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlvke 156
                                      ++l   +sn+r+++sL+++lk++++v+i+++DTR+l++ lRekg+++++i   ++++ ++ ++ak+ p +k+++l+ke
  lcl|FitnessBrowser__PV4:5210398  92 RDLPLLASNFRNEQSLSDYLKSNNVVGIADIDTRKLTRILREKGAQAGAILVGDMDEAKALAAAKAFPGLKGMDLAKE 169
                                      ****************************************************************************** PP

                        TIGR01368 157 vstkeayeleq...........kakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgills 223
                                      v+t+++y++++           ++ +++ k++vv++d+GvK+nilr+Lv+rg++vtvvpa+t+a+e+ ++npdgi+ls
  lcl|FitnessBrowser__PV4:5210398 170 VTTQKQYQWRSgswrlvgglpsDTPESELKYKVVAYDYGVKRNILRMLVDRGCDVTVVPAQTPAAEVLAMNPDGIFLS 247
                                      **********987777666554356666679*********************************************** PP

                        TIGR01368 224 nGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavd 301
                                      nGPGdP+ +++aie ++++l+++iP+fGIclGhqllala+gakt+k+kfGh+GaNhpv +l++g+v+itsqNHg+a d
  lcl|FitnessBrowser__PV4:5210398 248 NGPGDPEPCDYAIEAIQAFLKTDIPLFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNLEKGNVMITSQNHGFAAD 325
                                      ****************************************************************************** PP

                        TIGR01368 302 eeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                      e sl+++ ++vth++l+Dg+++g++ +++p+fs Q HPeaspGphd++ lFd+f+eli+
  lcl|FitnessBrowser__PV4:5210398 326 ETSLPAN-VKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGPHDAAPLFDHFIELIE 383
                                      ***8866.************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (390 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: 11.95
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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