Alignments for a candidate for carA in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Desulfobulbus mediterraneus DSM 13871

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate WP_028584701.1 G494_RS0111760 carbamoyl-phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>NCBI__GCF_000429965.1:WP_028584701.1
          Length = 371

 Score =  365 bits (937), Expect = e-105
 Identities = 186/371 (50%), Positives = 242/371 (65%), Gaps = 3/371 (0%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A + LEDG++   KSF  PG  + E+VFNTS++GYQE+LTDPSY GQ V MT P IGN G
Sbjct: 3   ALIGLEDGTVISGKSFTGPGEVMGEMVFNTSMSGYQEVLTDPSYTGQLVTMTYPLIGNYG 62

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           VN +D ES        ++R      SN R T TL D L    ++G+   DTR +TR LR+
Sbjct: 63  VNEEDMESAGVHPRAFLMREYQALPSNHRATGTLVDLLQRHQVLGIEGFDTRMLTRLLRK 122

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSW-DIVGIDLISDVSCKSPYEWVDKTNAEWDFNTNS 236
            G++   +STE     D L+  +RSW  +VG D+++ VSC  PY W  +   E      S
Sbjct: 123 SGAMKAAISTEDLD-GDSLVAKARSWAGLVGRDMVARVSCARPYLWTAEGPREAAAFPAS 181

Query: 237 RDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGPGDPS 296
               +++V+A DFG K N LR LS YGCQ+ VVP+T  AAE L + PDGI  SNGPGDP 
Sbjct: 182 GSA-AFRVVALDFGAKYNQLRLLSQYGCQVMVVPATTGAAEILALQPDGIFLSNGPGDPD 240

Query: 297 AVPYAVETVKELLGKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRTGQVEI 356
            V   VE V++LLGK P++GIC+GHQ+L  A GG T+K+KFGH GGN PV++  TG+VEI
Sbjct: 241 GVQGVVENVRQLLGKKPIFGICLGHQMLALAYGGSTYKLKFGHRGGNQPVKDLTTGKVEI 300

Query: 357 SAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHDSDNAF 416
           +AQNH + VDP SLP  VEVTH+NLND S  G+   +    S+QYHPE +PGPHD++  F
Sbjct: 301 TAQNHGFCVDPESLPPEVEVTHINLNDNSLEGMRHRDYPAFSVQYHPEYAPGPHDAEYLF 360

Query: 417 REFIELMKRSK 427
             FIELM++S+
Sbjct: 361 SRFIELMQQSR 371


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: 506
Number of extensions: 22
Number of successful extensions: 2
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: 371
Length adjustment: 31
Effective length of query: 399
Effective length of database: 340
Effective search space:   135660
Effective search space used:   135660
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_028584701.1 G494_RS0111760 (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.26094.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-151  489.2   0.0   4.1e-151  489.0   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028584701.1  G494_RS0111760 carbamoyl-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028584701.1  G494_RS0111760 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.0   0.0  4.1e-151  4.1e-151       2     360 ..       4     368 ..       3     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 489.0 bits;  conditional E-value: 4.1e-151
                                 TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskk 70 
                                                + ledGtv++gksf  ++ev+Ge+vFnTsm+GYqE+ltDpsY+gq+v++typlignygvneed+es  
  lcl|NCBI__GCF_000429965.1:WP_028584701.1   4 LIGLEDGTVISGKSFTGPGEVMGEMVFNTSMSGYQEVLTDPSYTGQLVTMTYPLIGNYGVNEEDMESAG 72 
                                               5779***************************************************************** PP

                                 TIGR01368  71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelv 139
                                               ++ ++++++e+++ +sn+ra+ +L + l+++++ +ieg DTR+l++ lR++g+mka+iste+ + ++lv
  lcl|NCBI__GCF_000429965.1:WP_028584701.1  73 VHPRAFLMREYQALPSNHRATGTLVDLLQRHQVLGIEGFDTRMLTRLLRKSGAMKAAISTEDLDGDSLV 141
                                               ********************************************************************* PP

                                 TIGR01368 140 ekakespkvkevnlvkevstkeayeleq...k....akkegkk.lrvvvidlGvKenilreLvkrgvev 200
                                               +ka++ + + + ++v++vs++++y +++   +      ++g+   rvv++d+G K n+lr L+++g++v
  lcl|NCBI__GCF_000429965.1:WP_028584701.1 142 AKARSWAGLVGRDMVARVSCARPYLWTAegpReaaaFPASGSAaFRVVALDFGAKYNQLRLLSQYGCQV 210
                                               ***************************955515555444555559************************ PP

                                 TIGR01368 201 tvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyk 269
                                               +vvpa+t a+ei +l+pdgi+lsnGPGdP+ v+ ++e+v++ll+ k+PifGIclGhq+lala+g++tyk
  lcl|NCBI__GCF_000429965.1:WP_028584701.1 211 MVVPATTGAAEILALQPDGIFLSNGPGDPDGVQGVVENVRQLLG-KKPIFGICLGHQMLALAYGGSTYK 278
                                               ********************************************.************************ PP

                                 TIGR01368 270 lkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyH 338
                                               lkfGhrG+N+pvkdl+tg+veit+qNHg+ vd+esl+ e +evth nlnD+++eg++h+++p+fsvQyH
  lcl|NCBI__GCF_000429965.1:WP_028584701.1 279 LKFGHRGGNQPVKDLTTGKVEITAQNHGFCVDPESLPPE-VEVTHINLNDNSLEGMRHRDYPAFSVQYH 346
                                               ***********************************9876.***************************** PP

                                 TIGR01368 339 PeaspGphdteylFdefvelik 360
                                               Pe +pGphd+eylF++f+el++
  lcl|NCBI__GCF_000429965.1:WP_028584701.1 347 PEYAPGPHDAEYLFSRFIELMQ 368
                                               ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (371 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.83
//
[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