Alignments for a candidate for glcD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcD in Herbaspirillum seropedicae SmR1

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate HSERO_RS19105 HSERO_RS19105 FAD-binding protein

Query= reanno::Cup4G11:RR42_RS17300
         (497 letters)



>FitnessBrowser__HerbieS:HSERO_RS19105
          Length = 495

 Score =  730 bits (1885), Expect = 0.0
 Identities = 366/497 (73%), Positives = 417/497 (83%), Gaps = 2/497 (0%)

Query: 1   MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALP 60
           MNAP + S     AR+  ++  L +++P   +L   EDT PYECDGLAAYRQ+PM V LP
Sbjct: 1   MNAPVQPSFAP--ARQREVVDALRRVVPAHCVLCDEEDTRPYECDGLAAYRQLPMVVVLP 58

Query: 61  DNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTA 120
           +NE QV AI++ CH+LQV +VPRGAGT LSGGA PIA G+V+S AKF +I+ +D  SRTA
Sbjct: 59  ENEAQVVAIMKTCHALQVQIVPRGAGTGLSGGATPIADGVVVSTAKFNQILQMDKYSRTA 118

Query: 121 VVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV 180
           VVQPGVRNLAISEAAA + LYYAPDPSSQIAC+IGGNV+ENSGGVHCLKYGLTVHNVLRV
Sbjct: 119 VVQPGVRNLAISEAAAPHGLYYAPDPSSQIACSIGGNVAENSGGVHCLKYGLTVHNVLRV 178

Query: 181 RAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD 240
           R VT+EG+VVE GS A DAPGLDLLA  IGSEGML VVTEV+VKL+PKPQ A+VIMASFD
Sbjct: 179 RMVTIEGEVVELGSGALDAPGLDLLAVFIGSEGMLGVVTEVTVKLVPKPQAARVIMASFD 238

Query: 241 DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV 300
           DV KGGNAVA+VI AGIIPAGLEMMDK ++  VE FV+AGYD+DA AILLCESDGT EEV
Sbjct: 239 DVVKGGNAVANVIAAGIIPAGLEMMDKTSSRMVEPFVKAGYDIDAEAILLCESDGTVEEV 298

Query: 301 AEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKH 360
            EE+ RM++VL ASGA+ I  SQSE ERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRK 
Sbjct: 299 EEEIGRMTDVLNASGATAIACSQSEAERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKK 358

Query: 361 IGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVE 420
           +  +L  I EME+KYGLRC NVFHAGDGN+HPLILFD    DE+HRAELFG++ILE CVE
Sbjct: 359 LAQVLLGIAEMEKKYGLRCANVFHAGDGNLHPLILFDANIADEFHRAELFGAEILELCVE 418

Query: 421 LGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYG 480
           +GGT+TGEHGVG+EK+NSMCVQFS  ER+ FF +K AFDPA LLNPDKAIPTL RCAEYG
Sbjct: 419 VGGTITGEHGVGIEKINSMCVQFSPAERETFFKLKRAFDPAFLLNPDKAIPTLHRCAEYG 478

Query: 481 RMHVKRGLLPHPDLPRF 497
           +MHV+RG L  PDLPRF
Sbjct: 479 KMHVQRGQLRFPDLPRF 495


Lambda     K      H
   0.319    0.136    0.402 

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: 750
Number of extensions: 20
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: 497
Length of database: 495
Length adjustment: 34
Effective length of query: 463
Effective length of database: 461
Effective search space:   213443
Effective search space used:   213443
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: 52 (24.6 bits)

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

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

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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