Alignments for a candidate for maiA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for maiA in Herbaspirillum seropedicae SmR1

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate HSERO_RS05615 HSERO_RS05615 maleylacetoacetate isomerase

Query= reanno::psRCH2:GFF3446
         (219 letters)



>FitnessBrowser__HerbieS:HSERO_RS05615
          Length = 215

 Score =  233 bits (593), Expect = 3e-66
 Identities = 116/215 (53%), Positives = 149/215 (69%), Gaps = 5/215 (2%)

Query: 6   TLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPLLVDEG 65
           TLY Y+RSSA+YRVRIAL+LK L Y  VPVHL+  GG+Q    +  +NP  LVP+L +EG
Sbjct: 3   TLYSYFRSSASYRVRIALHLKDLPYETVPVHLLNQGGEQLLPAFTEINPHALVPVLAEEG 62

Query: 66  NGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYLS 125
           +    +SQSLA+LE L+E  P P+LLP D  +RA +R+L++ IAC+IHPLNNLRVL+YL 
Sbjct: 63  H---YVSQSLAMLELLEERHPTPSLLPGDAFQRAHIRALSLAIACDIHPLNNLRVLKYLK 119

Query: 126 AELGVDDEAKNAWYRHWVSQGLAAVEQGL--ETFGDKLSLNDRPGYLEACLVPQVYNARR 183
            ELG+DDE KNAW  HW++ G  A+E+ L  +T      + D P   + CLVPQ++NARR
Sbjct: 120 RELGMDDERKNAWIAHWINLGFTALERQLAADTTRGHFCVGDAPTMADCCLVPQIFNARR 179

Query: 184 FACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218
           F  D+A YP +  I   C  LPAFQQA P  QPDA
Sbjct: 180 FEVDMAPYPTLCAIEQACHALPAFQQAHPAQQPDA 214


Lambda     K      H
   0.321    0.137    0.412 

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: 200
Number of extensions: 9
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: 219
Length of database: 215
Length adjustment: 22
Effective length of query: 197
Effective length of database: 193
Effective search space:    38021
Effective search space used:    38021
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: 45 (21.9 bits)

Align candidate HSERO_RS05615 HSERO_RS05615 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))

# 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/TIGR01262.hmm
# target sequence database:        /tmp/gapView.1819.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01262  [M=211]
Accession:   TIGR01262
Description: maiA: maleylacetoacetate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    3.2e-93  297.2   0.0    3.5e-93  297.1   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05615  HSERO_RS05615 maleylacetoacetate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05615  HSERO_RS05615 maleylacetoacetate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.1   0.0   3.5e-93   3.5e-93       1     210 [.       3     214 ..       3     215 .] 0.98

  Alignments for each domain:
  == domain 1  score: 297.1 bits;  conditional E-value: 3.5e-93
                                  TIGR01262   1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSl 67 
                                                +lYsyfrSsasyRvRiaL Lk++ ye+vpv+Ll++ Geq  ++f+++NP +lvP+L  + g+ ++qSl
  lcl|FitnessBrowser__HerbieS:HSERO_RS05615   3 TLYSYFRSSASYRVRIALHLKDLPYETVPVHLLNQgGEQLLPAFTEINPHALVPVLAEE-GHYVSQSL 69 
                                                59*********************************9*********************99.6******* PP

                                  TIGR01262  68 AiieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwi 135
                                                A++e Lee++p+p+Llp d+ +ra+ ral+l+iacdihPl+Nlrvl++l+++lg+d+e+k++w++hwi
  lcl|FitnessBrowser__HerbieS:HSERO_RS05615  70 AMLELLEERHPTPSLLPGDAFQRAHIRALSLAIACDIHPLNNLRVLKYLKRELGMDDERKNAWIAHWI 137
                                                ******************************************************************** PP

                                  TIGR01262 136 ekGlaalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqe 201
                                                + G++alE+ l+  +++g+fcvGd++t+ad+cLvpq+ nA+rfevd+a+yPtl +ie+a+++lpafq+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05615 138 NLGFTALERQLAadTTRGHFCVGDAPTMADCCLVPQIFNARRFEVDMAPYPTLCAIEQACHALPAFQQ 205
                                                *********99988899*************************************************** PP

                                  TIGR01262 202 ahpenqpdt 210
                                                ahp++qpd+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05615 206 AHPAQQPDA 214
                                                ********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (215 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.37
//
[ok]

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

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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

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