Alignments for a candidate for hutG in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG in Halomonas desiderata SP1

Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate WP_086509680.1 BZY95_RS09390 formimidoylglutamase

Query= reanno::Koxy:BWI76_RS08725
         (318 letters)



>NCBI__GCF_002151265.1:WP_086509680.1
          Length = 319

 Score =  230 bits (587), Expect = 3e-65
 Identities = 142/305 (46%), Positives = 181/305 (59%), Gaps = 14/305 (4%)

Query: 12  WQGRDDSAEAANALRLFQTIVRAERFEPEMLAGDIALLGFACDEGVRRNKGRTGAERGPE 71
           W GR+D     ++LR  Q I       P+   G  AL+GFA D GV RN+GR GA  GP 
Sbjct: 14  WAGREDPEP--DSLRWHQVITPVR---PDSAPG-AALVGFASDAGVARNQGRVGAAEGPR 67

Query: 72  TLRRALANMASHDGHDRCVDMGTIHV-ADDALEAAQQALREAVTACQRAGKRTLVLGGGH 130
            +RRALA +A H       D G +    +D LEAAQQ L + + +    G + LVLGGGH
Sbjct: 68  AIRRALAPLAWHRSAP-VFDAGDVSCHGNDDLEAAQQRLADRIASLLARGHQPLVLGGGH 126

Query: 131 ETAFGHGAGVLDAFPGE-----EVGIINLDAHLDLRIADRA-SSGTPFRQLALACEAQRR 184
           E AFG  +G+   F  E      +GIINLDAH DLR      SSGTPF Q+A  C A+  
Sbjct: 127 EVAFGSWSGLARHFEAEGEAHPRIGIINLDAHFDLRDPTHVRSSGTPFAQIAAECHARDW 186

Query: 185 AFHYACIGVSRAANTQALLDEAARRGVTIIEDLDVLNAFEARAIPELARNIARYDRLYLT 244
            F YAC+GVSRA+NT+AL   A    V + ED ++        + +L R +AR D LYL+
Sbjct: 187 PFRYACLGVSRASNTRALFTRARELNVLVREDHEIDALRLDAIVRDLQRFMARCDHLYLS 246

Query: 245 IDLDVLPAREMPAVSAPAALGIPLATLLRIVEPLCRSGKLQAVDLVEFNPQYDIDSQGAR 304
           IDLDVLPA E P VSAPAA G+PLA +  ++E +  SGKL+  D+ E NP +DID + A+
Sbjct: 247 IDLDVLPAAEAPGVSAPAARGVPLALIEPLLEAVRDSGKLRLADVAELNPSFDIDGRTAK 306

Query: 305 AAARL 309
           AAARL
Sbjct: 307 AAARL 311


Lambda     K      H
   0.322    0.135    0.408 

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: 293
Number of extensions: 20
Number of successful extensions: 6
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: 318
Length of database: 319
Length adjustment: 27
Effective length of query: 291
Effective length of database: 292
Effective search space:    84972
Effective search space used:    84972
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_086509680.1 BZY95_RS09390 (formimidoylglutamase)
to HMM TIGR01227 (hutG: formimidoylglutamase (EC 3.5.3.8))

# 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.carbon/TIGR01227.hmm
# target sequence database:        /tmp/gapView.22967.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01227  [M=307]
Accession:   TIGR01227
Description: hutG: formimidoylglutamase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-101  325.8   0.0   1.6e-101  325.5   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509680.1  BZY95_RS09390 formimidoylglutama


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509680.1  BZY95_RS09390 formimidoylglutamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.5   0.0  1.6e-101  1.6e-101       3     304 ..      16     314 ..      14     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 325.5 bits;  conditional E-value: 1.6e-101
                                 TIGR01227   3 grldleeaskkrrdeqvakvvdlveledaqdekgvaliGvaldkgvirnkGrtGAkeaPsairqalanl 71 
                                               gr d+e  +++ r++qv+++v +      +  +g+al+G+a+d+gv+rn+Gr+GA e+P air+ala l
  lcl|NCBI__GCF_002151265.1:WP_086509680.1  16 GREDPE--PDSLRWHQVITPVRP------DSAPGAALVGFASDAGVARNQGRVGAAEGPRAIRRALAPL 76 
                                               555554..56899******9999......7789************************************ PP

                                 TIGR01227  72 gdlvasealyDlGdivleg.ddlvdaqkevaqavaelladarvvvllGGdneiayatikalaqa..akg 137
                                                +++ s ++ D+Gd+ ++g ddl++aq+ +a ++a+lla ++++++lGG++e+a+ +  +la++  a+g
  lcl|NCBI__GCF_002151265.1:WP_086509680.1  77 -AWHRSAPVFDAGDVSCHGnDDLEAAQQRLADRIASLLARGHQPLVLGGGHEVAFGSWSGLARHfeAEG 144
                                               .****************96378******************************************76555 PP

                                 TIGR01227 138 ek..riGvinfDAHfDlRavederptsGTpfrqlldeeqaed..fhlivlGirrfsntqalfdyakkkg 202
                                               e   riG+in+DAHfDlR    +  +sGTpf q++ e+ a d  f +++lG++r+snt alf +a++++
  lcl|NCBI__GCF_002151265.1:WP_086509680.1 145 EAhpRIGIINLDAHFDLRDPT-HVRSSGTPFAQIAAECHARDwpFRYACLGVSRASNTRALFTRARELN 212
                                               5589***************99.67799****************************************** PP

                                 TIGR01227 203 vryvtddalaelsletikdileefldevDfiyltvdlDVldaasAPGvsApaagGleleellelvkria 271
                                               v + +d+++ +l l+ i   l++f+  +D++yl++dlDVl+aa APGvsApaa+G+ l  +++l++++ 
  lcl|NCBI__GCF_002151265.1:WP_086509680.1 213 VLVREDHEIDALRLDAIVRDLQRFMARCDHLYLSIDLDVLPAAEAPGVSAPAARGVPLALIEPLLEAVR 281
                                               ********************************************************************* PP

                                 TIGR01227 272 asdkvrgveivEvnPtlDaddrTarlaArlvah 304
                                                s+k+r+++++E+nP++D+d+rTa++aArl++ 
  lcl|NCBI__GCF_002151265.1:WP_086509680.1 282 DSGKLRLADVAELNPSFDIDGRTAKAAARLIHR 314
                                               *******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (319 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: 9.63
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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

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 catabolism of small carbon sources