Alignments for a candidate for carA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Pedobacter sp. GW460-11-11-14-LB5

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate CA265_RS15240 CA265_RS15240 carbamoyl phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Pedo557:CA265_RS15240
          Length = 370

 Score =  310 bits (794), Expect = 4e-89
 Identities = 167/373 (44%), Positives = 229/373 (61%), Gaps = 18/373 (4%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           A+L+L DGT F+G+A G  G+  GE+ FNT MTGYQEI TDPSY  QI+  T  HIGN G
Sbjct: 9   AILLLADGTVFYGKAAGKIGTTTGEICFNTGMTGYQEIFTDPSYFGQIMVTTNAHIGNYG 68

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            +  + ES  +   GLV ++  ++ S    TE +  Y +  N+VAI+DIDTR L R +R+
Sbjct: 69  IHKDEIESGSIKIAGLVCKNYNIVYSRKEATESIQDYFQNDNLVAISDIDTRALVRHIRD 128

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGA N  II+ +  D     +K    P + G++L+ +V+T E Y +         G PEA
Sbjct: 129 KGAMNA-IISSEITDLEELKQKLAEVPSMEGLELSSKVSTTEPYFY---------GNPEA 178

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
             +      V A D G K+NILR   +R   + + PA+TS  ++ K +PDG F+SNGPGD
Sbjct: 179 SLK------VAALDLGIKKNILRNFENRDIYVQVFPAKTSFAEMEKFSPDGYFISNGPGD 232

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           P+   YA+  I   L  D P+FGICLGHQLLA A+G  T+KM  GH G NHPVK++ KN 
Sbjct: 233 PSVMPYAVETITAILAVDKPLFGICLGHQLLAEANGIGTMKMFNGHRGLNHPVKNIIKNH 292

Query: 305 VMITAQNHGFAV--DEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHD 362
             +T+QNHGF V  DE      + +TH +L D +++GI    K AFS Q HPE+SPGPHD
Sbjct: 293 CEVTSQNHGFGVIPDEVRNSDKVEITHVNLNDKSIEGIRVKGKKAFSVQYHPESSPGPHD 352

Query: 363 AAPLFDHFIELIE 375
           +  LFD F+++++
Sbjct: 353 SRYLFDDFVDVMK 365


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: 386
Number of extensions: 16
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: 370
Length adjustment: 30
Effective length of query: 352
Effective length of database: 340
Effective search space:   119680
Effective search space used:   119680
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 CA265_RS15240 CA265_RS15240 (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.32671.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     3e-141  456.5   0.4   3.4e-141  456.3   0.4    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15240  CA265_RS15240 carbamoyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15240  CA265_RS15240 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.3   0.4  3.4e-141  3.4e-141       1     360 [.       9     365 ..       9     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.3 bits;  conditional E-value: 3.4e-141
                                  TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaes 68 
                                                a+l+l+dGtvf gk+ g+ ++++Ge++FnT+mtGYqEi+tDpsY gqi+v t+ +ignyg++++++es
  lcl|FitnessBrowser__Pedo557:CA265_RS15240   9 AILLLADGTVFYGKAAGKIGTTTGEICFNTGMTGYQEIFTDPSYFGQIMVTTNAHIGNYGIHKDEIES 76 
                                                689***************************************************************** PP

                                  TIGR01368  69 kkikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekseke 136
                                                 +ik++glv k+++  +s  +a+es+++++++ ++vai ++DTRalv+++R+kg+m+a+is+e ++ e
  lcl|FitnessBrowser__Pedo557:CA265_RS15240  77 GSIKIAGLVCKNYNIVYSRKEATESIQDYFQNDNLVAISDIDTRALVRHIRDKGAMNAIISSEITDLE 144
                                                ******************************************************************** PP

                                  TIGR01368 137 elvekakespkvkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvp 204
                                                el++k++e p++++++l ++vst+e+y + +     + +l+v+++dlG+K+nilr++ +r++ v+v+p
  lcl|FitnessBrowser__Pedo557:CA265_RS15240 145 ELKQKLAEVPSMEGLELSSKVSTTEPYFYGN----PEASLKVAALDLGIKKNILRNFENRDIYVQVFP 208
                                                ***************************9995....677789*************************** PP

                                  TIGR01368 205 adtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkf 272
                                                a+ts++e++k++pdg ++snGPGdP+ + +a+et+ ++l  ++P+fGIclGhqlla a g  t+k+  
  lcl|FitnessBrowser__Pedo557:CA265_RS15240 209 AKTSFAEMEKFSPDGYFISNGPGDPSVMPYAVETITAILAVDKPLFGICLGHQLLAEANGIGTMKMFN 276
                                                ******************************************************************** PP

                                  TIGR01368 273 GhrGaNhpvkdlktgrveitsqNHgyavdeeslk.eeelevthvnlnDgtveglehkelpvfsvQyHP 339
                                                GhrG Nhpvk+++++++e+tsqNHg+ v ++ ++ ++++e+thvnlnD+++eg++ k +++fsvQyHP
  lcl|FitnessBrowser__Pedo557:CA265_RS15240 277 GHRGLNHPVKNIIKNHCEVTSQNHGFGVIPDEVRnSDKVEITHVNLNDKSIEGIRVKGKKAFSVQYHP 344
                                                ***************************99988851678****************************** PP

                                  TIGR01368 340 easpGphdteylFdefvelik 360
                                                e+spGphd++ylFd+fv+ +k
  lcl|FitnessBrowser__Pedo557:CA265_RS15240 345 ESSPGPHDSRYLFDDFVDVMK 365
                                                *****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (370 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: 9.54
//
[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