GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Marinobacter adhaerens HP15

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate GFF1553 HP15_1515 6-phosphogluconate dehydrogenase domain protein

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__Marino:GFF1553
          Length = 290

 Score =  147 bits (370), Expect = 4e-40
 Identities = 92/274 (33%), Positives = 147/274 (53%), Gaps = 8/274 (2%)

Query: 1   MTDIAFLGLGNMGGPMAANLLKAGHRVNVFD-LQPKAVLGLVEQGAQGADSALQCCEGAE 59
           MT  AF+GLG MG PMA +L KAG  V V++    KA     E       +  +   GA+
Sbjct: 1   MTTAAFIGLGVMGYPMAGHLAKAGLDVRVWNRTNAKAEQWASEYSGTSCTTIAETVRGAD 60

Query: 60  VVISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDA 119
           +V++ + A   + ++Y GD+G+LA  +   +L+D +T +   A  +AEAA+   +  +DA
Sbjct: 61  IVLTCVGADTDLMAVYEGDEGILANASEGAVLVDHTTASAGIAEYLAEAASKNNMGFVDA 120

Query: 120 PVSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLG 179
           PVSGG  GA  G L+ + GG  + +A+A PV+E+  R +   G  G+GQ  K+ N + + 
Sbjct: 121 PVSGGQQGAENGKLTIMCGGSEQDYAKAEPVMEHYARALNRMGPAGSGQKTKMVNQIAIA 180

Query: 180 ILMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGF 239
            L+ G +EAL    +  LD A + +V+ + +  +W +   +   G M     +  +  GF
Sbjct: 181 GLVQGLSEALHFAEQAELDVAKVVDVISKGAAQSWQMENRS---GTM----IAGEFEHGF 233

Query: 240 QVRLMNKDLGLALANAQAVQASTPLGALARNLFS 273
            V  M KDLG+ L  A+ V AS P+ AL    ++
Sbjct: 234 AVDWMRKDLGICLEEARKVNASLPVTALVDQFYA 267


Lambda     K      H
   0.317    0.135    0.395 

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: 250
Number of extensions: 14
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: 298
Length of database: 290
Length adjustment: 26
Effective length of query: 272
Effective length of database: 264
Effective search space:    71808
Effective search space used:    71808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

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:

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:

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:

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:

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