Alignments for a candidate for argI in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Saccharomonospora cyanea NA-134

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_005457884.1 SACCYDRAFT_RS16635 ornithine carbamoyltransferase

Query= BRENDA::P0A5M9
         (307 letters)



>NCBI__GCF_000244975.1:WP_005457884.1
          Length = 308

 Score =  439 bits (1128), Expect = e-128
 Identities = 221/306 (72%), Positives = 250/306 (81%), Gaps = 1/306 (0%)

Query: 1   MIRHFLRDDDLSPAEQAEVLELAAELKKDPVSRRPLQGPRGVAVIFDKNSTRTRFSFELG 60
           M RHFLRDDDL+P+EQAEVL+LAA+LK+ P     L GP+ VAVIF+KNSTRTRFSFE G
Sbjct: 1   MPRHFLRDDDLTPSEQAEVLDLAAKLKQQPYGDA-LAGPKTVAVIFEKNSTRTRFSFEAG 59

Query: 61  IAQLGGHAVVVDSGSTQLGRDETLQDTAKVLSRYVDAIVWRTFGQERLDAMASVATVPVI 120
           I+QLGGHAVVVD  S QLGR+ET+ DTA+VLSRY D +VWRTFGQER+D  A+ ATVPV+
Sbjct: 60  ISQLGGHAVVVDGHSMQLGREETIGDTARVLSRYTDLVVWRTFGQERIDEFAAAATVPVV 119

Query: 121 NALSDEFHPCQVLADLQTIAERKGALRGLRLSYFGDGANNMAHSLLLGGVTAGIHVTVAA 180
           NAL+DEFHPCQ+LADL T+ ERKGAL GL L+Y GDGANNMAHSLLLGGVTAG+HV VAA
Sbjct: 120 NALTDEFHPCQILADLFTVRERKGALAGLTLTYLGDGANNMAHSLLLGGVTAGMHVRVAA 179

Query: 181 PEGFLPDPSVRAAAERRAQDTGASVTVTADAHAAAAGADVLVTDTWTSMGQENDGLDRVK 240
           PEGF P P V  A  +RA++TG S  V  D HAA  GADV+ TD WTSMGQE DG DRV 
Sbjct: 180 PEGFHPLPWVLDAVAKRAEETGGSAAVFTDPHAAVDGADVVTTDAWTSMGQEGDGKDRVT 239

Query: 241 PFRPFQLNSRLLALADSDAIVLHCLPAHRGDEITDAVMDGPASAVWDEAENRLHAQKALL 300
           PF P+Q+N+ LLA    D IVLH LPAHRG EITD V+DGPASAVWDEAENRLHAQKALL
Sbjct: 240 PFLPYQVNTDLLARTGKDTIVLHDLPAHRGMEITDEVIDGPASAVWDEAENRLHAQKALL 299

Query: 301 VWLLER 306
           VWLL +
Sbjct: 300 VWLLRQ 305


Lambda     K      H
   0.319    0.133    0.387 

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: 327
Number of extensions: 8
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: 307
Length of database: 308
Length adjustment: 27
Effective length of query: 280
Effective length of database: 281
Effective search space:    78680
Effective search space used:    78680
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 WP_005457884.1 SACCYDRAFT_RS16635 (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.31947.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-115  370.2   0.0   4.3e-115  370.0   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005457884.1  SACCYDRAFT_RS16635 ornithine car


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005457884.1  SACCYDRAFT_RS16635 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.0   0.0  4.3e-115  4.3e-115       1     303 [.       3     303 ..       3     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 370.0 bits;  conditional E-value: 4.3e-115
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 
                                               rh+l   dl+++e  e+l+la+klk++ + +   +    kt+a+iFek+stRtR sfe+++ +lG++++
  lcl|NCBI__GCF_000244975.1:WP_005457884.1   3 RHFLRDDDLTPSEQAEVLDLAAKLKQQPYGD---ALAGPKTVAVIFEKNSTRTRFSFEAGISQLGGHAV 68 
                                               799999********************99983...44456****************************** PP

                                 TIGR00658  70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138
                                               +++ +++qlgr+e+i Dtarvlsry d +v R++ +e + e+a  a+vPv+n+Ltd++hPcqilaDl+t
  lcl|NCBI__GCF_000244975.1:WP_005457884.1  69 VVDGHSMQLGREETIGDTARVLSRYTDLVVWRTFGQERIDEFAAAATVPVVNALTDEFHPCQILADLFT 137
                                               ********************************************************************* PP

                                 TIGR00658 139 ikeklgklkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklel 206
                                               ++e++g+l +++l+y+GD+ nn+a+slll++++ G++v+va+Peg++p + +++   k a+e+gg+  +
  lcl|NCBI__GCF_000244975.1:WP_005457884.1 138 VRERKGALAGLTLTYLGDGaNNMAHSLLLGGVTAGMHVRVAAPEGFHPLPWVLDAVAKRAEETGGSAAV 206
                                               *******************9************************************************* PP

                                 TIGR00658 207 tedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtde 275
                                                 dp+ av +adv+ tD w+smG+e + ++r+  + pyqvn++ll+ + +++++lh LPa+rG+e+tde
  lcl|NCBI__GCF_000244975.1:WP_005457884.1 207 FTDPHAAVDGADVVTTDAWTSMGQEGDGKDRVTPFLPYQVNTDLLARTGKDTIVLHDLPAHRGMEITDE 275
                                               ********************************************************************* PP

                                 TIGR00658 276 vlegeasivfdeaenRlhaqkavlkall 303
                                               v++g+as v+deaenRlhaqka+l++ll
  lcl|NCBI__GCF_000244975.1:WP_005457884.1 276 VIDGPASAVWDEAENRLHAQKALLVWLL 303
                                               *************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (308 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: 00:00:00.00
# Mc/sec: 11.32
//
[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