Alignments for a candidate for carA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Dinoroseobacter shibae DFL-12

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 3608998 Dshi_2387 carbamoyl-phosphate synthase, small subunit (RefSeq)

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Dino:3608998
          Length = 389

 Score =  377 bits (968), Expect = e-109
 Identities = 198/374 (52%), Positives = 253/374 (67%), Gaps = 13/374 (3%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           +A LVL DGT F+GR  GA G+   E+ FNT+MTGYQEI+TDPSY+ Q+VT T+PHIGN 
Sbjct: 9   TACLVLADGTVFYGRGFGAVGTTSAELCFNTAMTGYQEIMTDPSYAGQVVTFTFPHIGNT 68

Query: 64  GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123
           G    D+E++   A G+V++  P   SN+R    L+ +L R   + I  +DTR+LTR +R
Sbjct: 69  GVTAEDDEAADPVAAGMVVKWDPSEPSNWRAQGKLTEWLTRTGRIGIGGVDTRRLTRQIR 128

Query: 124 EKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTG 179
           ++GA +  +    +P+    LE    +ARAF GL G+DLA+EVT A++Y W +  W    
Sbjct: 129 QQGAPH--VALAHDPEGNFDLEALVAQARAFAGLEGVDLAREVTCAQSYRWDEQRWAW-- 184

Query: 180 GLPEAKKEDELPFH-VVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFL 238
             PE       P H VVA D+GAKRNILR L   GC +T++PA ++AEDVL  NPDG+FL
Sbjct: 185 --PEGYTRRTTPGHKVVALDYGAKRNILRCLASAGCDVTVMPATSTAEDVLAQNPDGVFL 242

Query: 239 SNGPGDPAPCD-YAITAIQKFLE-TDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHP 296
           SNGPGDPA    YA+  I+  LE +D+PVFGICLGHQ+LALA GA+TVKM  GHHG NHP
Sbjct: 243 SNGPGDPAATGKYAVPMIKGVLEASDVPVFGICLGHQMLALALGAQTVKMNHGHHGANHP 302

Query: 297 VKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEA 356
           VKD+E   V IT+ NHGF VD  TLP  +  TH+SLFDG+  GI  TD+P FS Q HPEA
Sbjct: 303 VKDLETGKVEITSMNHGFTVDSQTLPHGVVETHRSLFDGSNCGIRMTDRPVFSVQYHPEA 362

Query: 357 SPGPHDAAPLFDHF 370
           SPGP D+  LF+ F
Sbjct: 363 SPGPQDSYYLFERF 376


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: 493
Number of extensions: 19
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: 389
Length adjustment: 30
Effective length of query: 352
Effective length of database: 359
Effective search space:   126368
Effective search space used:   126368
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 3608998 Dshi_2387 (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.17805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-137  443.7   0.0   2.6e-137  443.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608998  Dshi_2387 carbamoyl-phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608998  Dshi_2387 carbamoyl-phosphate synthase, small subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.5   0.0  2.6e-137  2.6e-137       1     360 [.      10     381 ..      10     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 443.5 bits;  conditional E-value: 2.6e-137
                         TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglv 77 
                                       a lvl+dGtvf g++fga +++ +e++FnT+mtGYqEi+tDpsY+gq+v++t p+ign+gv++ed e+  + ++g+v
  lcl|FitnessBrowser__Dino:3608998  10 ACLVLADGTVFYGRGFGAVGTTSAELCFNTAMTGYQEIMTDPSYAGQVVTFTFPHIGNTGVTAEDDEAADPVAAGMV 86 
                                       579************************************************************************** PP

                         TIGR01368  78 vkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelvekakespkvkev 151
                                       vk   +e+sn+ra+ +L+e+l+++g ++i gvDTR l++++R++g+ + +++++ +     e lv++a++ + +++v
  lcl|FitnessBrowser__Dino:3608998  87 VKWDPSEPSNWRAQGKLTEWLTRTGRIGIGGVDTRRLTRQIRQQGAPHVALAHDPEGnfdLEALVAQARAFAGLEGV 163
                                       ***************************************************998865555789999999******** PP

                         TIGR01368 152 nlvkevstkeayeleqk........akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220
                                       +l++ev++++ y++ ++        +++++  ++vv++d+G K+nilr+L++ g++vtv+pa+++ae++ + npdg+
  lcl|FitnessBrowser__Dino:3608998 164 DLAREVTCAQSYRWDEQrwawpegyTRRTTPGHKVVALDYGAKRNILRCLASAGCDVTVMPATSTAEDVLAQNPDGV 240
                                       ***************9556666676666666699******************************************* PP

                         TIGR01368 221 llsnGPGdPaav.eeaietvkkllea.kiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqN 295
                                       +lsnGPGdPaa  ++a+ ++k +lea ++P+fGIclGhq+lalalga+t+k++ Gh+GaNhpvkdl+tg+veits N
  lcl|FitnessBrowser__Dino:3608998 241 FLSNGPGDPAATgKYAVPMIKGVLEAsDVPVFGICLGHQMLALALGAQTVKMNHGHHGANHPVKDLETGKVEITSMN 317
                                       *********776377899******9989************************************************* PP

                         TIGR01368 296 HgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                       Hg++vd+++l+++ +  th++l+Dg++ g+++++ pvfsvQyHPeaspGp+d+ ylF++f  +++
  lcl|FitnessBrowser__Dino:3608998 318 HGFTVDSQTLPHG-VVETHRSLFDGSNCGIRMTDRPVFSVQYHPEASPGPQDSYYLFERFAAAMA 381
                                       *********9877.889*******************************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (389 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: 8.67
//
[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