Alignments for a candidate for argI in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Caulobacter crescentus NA1000

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate CCNA_02325 CCNA_02325 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Caulo:CCNA_02325
          Length = 311

 Score =  320 bits (821), Expect = 2e-92
 Identities = 170/307 (55%), Positives = 206/307 (67%), Gaps = 9/307 (2%)

Query: 4   RHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTR-----PLEGKVLAMIFDKPSTRTRV 58
           RHF DL  +    LR +LDDA  RKA  K   + +     P + +VL+MIF K STRTR 
Sbjct: 5   RHFIDLWKLDGATLRLLLDDAHARKAARKGWPQGKVDADAPAKDRVLSMIFQKNSTRTRF 64

Query: 59  SFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENA 118
           SFD  MRQLGG  I+ T ++MQLGR ETI DTAKVLSR VDA+MIR  SH  +    + +
Sbjct: 65  SFDAAMRQLGGSAIISTASDMQLGRGETIEDTAKVLSRMVDAVMIRANSHADVERFAQVS 124

Query: 119 TVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNL 178
           TVP+INGLTD +HPCQ+MADI+T EEHRGP+AGKTIAW GDGNNV  S + A+    F L
Sbjct: 125 TVPIINGLTDKSHPCQIMADILTIEEHRGPIAGKTIAWVGDGNNVCSSFIHAAPLLGFEL 184

Query: 179 NVAVPEGSEPAQKHIDWSKAHG--GKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGH 236
            +A P     A  H D ++A G  GK+  T  P+ AV  AD VV D WVSMG        
Sbjct: 185 KIACP-AVYHADLH-DLARAEGLQGKVSMTTDPKAAVSGADVVVADTWVSMGDTDHDERL 242

Query: 237 NVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAV 296
               PYQV+ +LM  A  + +F+HCLPAHRGEEVTD V+DGP S+V+DEAENR+HAQK+V
Sbjct: 243 AALEPYQVDDRLMDLAAGNGVFLHCLPAHRGEEVTDAVLDGPRSLVWDEAENRIHAQKSV 302

Query: 297 LAWCLGA 303
           LAWC GA
Sbjct: 303 LAWCFGA 309


Lambda     K      H
   0.320    0.133    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: 335
Number of extensions: 10
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: 303
Length of database: 311
Length adjustment: 27
Effective length of query: 276
Effective length of database: 284
Effective search space:    78384
Effective search space used:    78384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate CCNA_02325 CCNA_02325 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

# 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/TIGR00658.hmm
# target sequence database:        /tmp/gapView.18971.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00658  [M=304]
Accession:   TIGR00658
Description: orni_carb_tr: ornithine carbamoyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-111  358.4   0.0   1.7e-111  358.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02325  CCNA_02325 ornithine carbamoyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02325  CCNA_02325 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.2   0.0  1.7e-111  1.7e-111       1     303 [.       5     307 ..       5     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 358.2 bits;  conditional E-value: 1.7e-111
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayelGaqv 68 
                                           rh+++l++l+ + l+ ll+ a+  k+++k   +     ++  k + l++iF+k+stRtR sf++a+ +lG+ +
  lcl|FitnessBrowser__Caulo:CCNA_02325   5 RHFIDLWKLDGATLRLLLDDAHARKAARKGWPQgkvdaDAPAKDRVLSMIFQKNSTRTRFSFDAAMRQLGGSA 77 
                                           8*********************9999887533333455778999***************************** PP

                             TIGR00658  69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltike 141
                                           ++  ++++qlgr+e+i+Dta+vlsr+vda+++R+++h dve +a+ ++vP+ingLtd++hPcqi+aD+lti+e
  lcl|FitnessBrowser__Caulo:CCNA_02325  78 IISTASDMQLGRGETIEDTAKVLSRMVDAVMIRANSHADVERFAQVSTVPIINGLTDKSHPCQIMADILTIEE 150
                                           ************************************************************************* PP

                             TIGR00658 142 klgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkav 214
                                           + g + + ++++vGD+nnv+ s++ aa +lG+++++a+P  ++ + + + +a    +   gk+++t dpk av
  lcl|FitnessBrowser__Caulo:CCNA_02325 151 HRGPIAGKTIAWVGDGNNVCSSFIHAAPLLGFELKIACPAVYHADLHDLARA----EGLQGKVSMTTDPKAAV 219
                                           ****************************************998765555554....6788************* PP

                             TIGR00658 215 kdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfde 287
                                           ++adv++ D+wvsmG+ ++  erl++l+pyqv+++l++la  + +flhCLPa+rGeevtd vl+g++s+v+de
  lcl|FitnessBrowser__Caulo:CCNA_02325 220 SGADVVVADTWVSMGDTDHD-ERLAALEPYQVDDRLMDLAAGNGVFLHCLPAHRGEEVTDAVLDGPRSLVWDE 291
                                           ***************98765.9*************************************************** PP

                             TIGR00658 288 aenRlhaqkavlkall 303
                                           aenR+haqk+vl++++
  lcl|FitnessBrowser__Caulo:CCNA_02325 292 AENRIHAQKSVLAWCF 307
                                           ************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (311 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: 5.09
//
[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