Alignments for a candidate for liuA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuA in Klebsiella michiganensis M5al

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate BWI76_RS02590 BWI76_RS02590 isovaleryl-CoA dehydrogenase

Query= SwissProt::P33224
         (541 letters)



>FitnessBrowser__Koxy:BWI76_RS02590
          Length = 545

 Score =  869 bits (2246), Expect = 0.0
 Identities = 422/537 (78%), Positives = 467/537 (86%)

Query: 1   MHWQTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGR 60
           MHWQTHTVFNQP PL NSNL+LSD AL EAV REGAGWD D LASIGQQLGTAESLELGR
Sbjct: 1   MHWQTHTVFNQPSPLCNSNLFLSDTALREAVVREGAGWDGDLLASIGQQLGTAESLELGR 60

Query: 61  LANVNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAAR 120
           LAN NPPELLRYDA G RLDDVRFHPAWHLLMQ LC NRVHNLAW+EDAR GAFVARAAR
Sbjct: 61  LANSNPPELLRYDATGSRLDDVRFHPAWHLLMQGLCANRVHNLAWQEDAREGAFVARAAR 120

Query: 121 FMLHAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLI 180
           FMLHAQVEAG+LCPITMTFAA PLL + LP PF DW +PLLSDRYD HL+PG QKRGLLI
Sbjct: 121 FMLHAQVEAGTLCPITMTFAAIPLLQRSLPRPFSDWLSPLLSDRYDPHLIPGNQKRGLLI 180

Query: 181 GMGMTEKQGGSDVMSNTTRAERLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFV 240
           GMGMTEKQGGSDV+SNTTRAE+  +G Y L+GHKWFFSVPQSDAHLVLAQ   GLSCFFV
Sbjct: 181 GMGMTEKQGGSDVLSNTTRAEKTAEGFYHLIGHKWFFSVPQSDAHLVLAQAPAGLSCFFV 240

Query: 241 PRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRF 300
           PR LPDGQRN + LERLKDKLGNR+NAS EVEF +A GWL+G EG+G+R ILKMGG+TRF
Sbjct: 241 PRLLPDGQRNGVHLERLKDKLGNRANASSEVEFFNACGWLVGEEGDGVRQILKMGGLTRF 300

Query: 301 DCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLAR 360
           DCALGSHA+MRRA+S+A+YHA QR  FG  L+ QP+MR VL +MAL+LEGQTA LFRLAR
Sbjct: 301 DCALGSHALMRRAYSVALYHALQRQAFGKNLVDQPMMRQVLGQMALRLEGQTAFLFRLAR 360

Query: 361 AWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPV 420
           AWDRR DA+EALWARLFTPAAKF ICK G+ FVAEAMEVLGG GYCEESELPRLYREMPV
Sbjct: 361 AWDRRDDAQEALWARLFTPAAKFAICKSGIAFVAEAMEVLGGSGYCEESELPRLYREMPV 420

Query: 421 NSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPAEE 480
           NSIWEGSGNIMCLDV+RVL KQ    +LL+    EVKGQ+R+FDRA R+LQQ LR+P EE
Sbjct: 421 NSIWEGSGNIMCLDVMRVLMKQPAALELLAAECAEVKGQNRHFDRAWRQLQQWLRRPLEE 480

Query: 481 LGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGGVRLSEQIQNDLLLRATG 537
            GREIT  ++LLG GAQ+L++ASPP+A+AWC++MLDTRGG+RL EQ  +DLLLRA G
Sbjct: 481 QGREITRLVYLLGVGAQVLRFASPPLAEAWCRMMLDTRGGMRLDEQTLDDLLLRAMG 537


Lambda     K      H
   0.324    0.138    0.428 

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: 973
Number of extensions: 26
Number of successful extensions: 1
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: 541
Length of database: 545
Length adjustment: 35
Effective length of query: 506
Effective length of database: 510
Effective search space:   258060
Effective search space used:   258060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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