Alignments for a candidate for carA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Klebsiella michiganensis M5al

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate BWI76_RS04465 BWI76_RS04465 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Koxy:BWI76_RS04465
          Length = 382

 Score =  734 bits (1896), Expect = 0.0
 Identities = 361/382 (94%), Positives = 372/382 (97%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           MIKSALLVLEDGTQFHGRAIGATG+AVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI
Sbjct: 1   MIKSALLVLEDGTQFHGRAIGATGTAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GNVGTN ADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR
Sbjct: 61  GNVGTNAADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           LLREKGAQNGCIIAGD+PDA LALEKA+AFPGLNGMDLAKEVTTAE YSWTQGSWTL G 
Sbjct: 121 LLREKGAQNGCIIAGDSPDAQLALEKAKAFPGLNGMDLAKEVTTAETYSWTQGSWTLAGD 180

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
           LPEAK E ELPFHVVAYDFGAKRNILRMLVDRGCRLT+VPAQTSAE+VLKMNPDGIFLSN
Sbjct: 181 LPEAKAESELPFHVVAYDFGAKRNILRMLVDRGCRLTVVPAQTSAEEVLKMNPDGIFLSN 240

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDPAPCDYAI AI KFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKD+
Sbjct: 241 GPGDPAPCDYAIDAITKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDM 300

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           + NVVMITAQNHGFAVDEA++PANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP
Sbjct: 301 DNNVVMITAQNHGFAVDEASMPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360

Query: 361 HDAAPLFDHFIELIEQYRKTAK 382
           HDAAPLFDHFIELIEQYR++AK
Sbjct: 361 HDAAPLFDHFIELIEQYRQSAK 382


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: 621
Number of extensions: 13
Number of successful extensions: 1
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: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 BWI76_RS04465 BWI76_RS04465 (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.23087.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.5e-157  507.8   0.0   8.6e-157  507.6   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04465  BWI76_RS04465 carbamoyl-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04465  BWI76_RS04465 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.6   0.0  8.6e-157  8.6e-157       1     360 [.       5     375 ..       5     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 507.6 bits;  conditional E-value: 8.6e-157
                               TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskki 71 
                                             a lvledGt+f+g+++ga++++vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ d+es+++
  lcl|FitnessBrowser__Koxy:BWI76_RS04465   5 ALLVLEDGTQFHGRAIGATGTAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTNAADEESSQV 75 
                                             579******************************************************************** PP

                               TIGR01368  72 kvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvek 141
                                             +++glv+++l   +sn+r++e+L+++lk+++ivai+++DTR+l++ lRekg+++++i + +s  ++ + ek
  lcl|FitnessBrowser__Koxy:BWI76_RS04465  76 HAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLREKGAQNGCIIAGDSPdAQLALEK 146
                                             *********************************************************99998834556899 PP

                               TIGR01368 142 akespkvkevnlvkevstkeayeleq..........kakkegkk.lrvvvidlGvKenilreLvkrgvevt 201
                                             ak+ p +++++l+kev+t+e+y+++q          +ak+e++   +vv++d+G K+nilr+Lv+rg+++t
  lcl|FitnessBrowser__Koxy:BWI76_RS04465 147 AKAFPGLNGMDLAKEVTTAETYSWTQgswtlagdlpEAKAESELpFHVVAYDFGAKRNILRMLVDRGCRLT 217
                                             *************************988877766553666666679************************* PP

                               TIGR01368 202 vvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkf 272
                                             vvpa+tsaee+ k+npdgi+lsnGPGdPa +++ai+ + k+le++iP+fGIclGhqllala+gakt+k+kf
  lcl|FitnessBrowser__Koxy:BWI76_RS04465 218 VVPAQTSAEEVLKMNPDGIFLSNGPGDPAPCDYAIDAITKFLETDIPVFGICLGHQLLALASGAKTVKMKF 288
                                             *********************************************************************** PP

                               TIGR01368 273 GhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeasp 343
                                             Gh+G+Nhpvkd++++ v+it+qNHg+avde+s++++ l+vth++l+Dgt++g++++++p+fs Q HPeasp
  lcl|FitnessBrowser__Koxy:BWI76_RS04465 289 GHHGGNHPVKDMDNNVVMITAQNHGFAVDEASMPAN-LRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358
                                             ********************************8865.********************************** PP

                               TIGR01368 344 GphdteylFdefvelik 360
                                             Gphd++ lFd+f+eli+
  lcl|FitnessBrowser__Koxy:BWI76_RS04465 359 GPHDAAPLFDHFIELIE 375
                                             **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (382 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: 6.96
//
[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