Alignments for a candidate for fadB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Klebsiella michiganensis M5al

Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate BWI76_RS13125 BWI76_RS13125 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::P76083
         (475 letters)



>FitnessBrowser__Koxy:BWI76_RS13125
          Length = 473

 Score =  667 bits (1722), Expect = 0.0
 Identities = 340/474 (71%), Positives = 387/474 (81%), Gaps = 2/474 (0%)

Query: 1   MMINVQTVAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGK 60
           M   + TVAVIGSGTMGAGIAEVAA+ GH VL++DI+ EA+ RAIDGI  RL SRV+RGK
Sbjct: 1   MSKTLPTVAVIGSGTMGAGIAEVAAAAGHPVLIFDIAPEAVVRAIDGIRQRLASRVSRGK 60

Query: 61  LTAETCERTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNT 120
           L  E  +  L RL+P  ++  LA A L+IEAASERLEVKKALF QLA +C P TLL +NT
Sbjct: 61  LATEQADALLARLVPAAELSNLADAQLIIEAASERLEVKKALFEQLAAICSPSTLLVSNT 120

Query: 121 SSISITAIAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQP 180
           SSISITAIAA IK+PERVAGLHFFNPAPVMKLVEVVSGLAT+ EVVEQLC+    WGKQP
Sbjct: 121 SSISITAIAAGIKHPERVAGLHFFNPAPVMKLVEVVSGLATSTEVVEQLCQWVSDWGKQP 180

Query: 181 VRCHSTPGFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQD 240
           VRC STPGFIVNRVARP+Y+EAWRALEEQVAAPEVIDAALRDG GFPMGPL LTDLIGQD
Sbjct: 181 VRCRSTPGFIVNRVARPFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQD 240

Query: 241 VNFAVTCSVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWRAEREAVVGLEAVSD 300
           VNFAVTCSVFNA WQ+RR+ PSL+QQEL + GRLGKKSG GVY W AE +    L AVS 
Sbjct: 241 VNFAVTCSVFNACWQDRRYQPSLLQQELALAGRLGKKSGQGVYRWPAEAQPERALAAVSA 300

Query: 301 SFSPMKVEKKSDGVTEIDDVLLIETQGETAQALAIRLARPVVVIDKMAGKVVTIAAAAVN 360
             +  ++  K D VTE+D++LL+ET GETA AL+++  RPVVV D  AG  V +A+A   
Sbjct: 301 ERAAKRI--KRDVVTELDEILLLETTGETALALSLQHGRPVVVYDHCAGDTVVLASAETT 358

Query: 361 PDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVAMIINEALDALQKGVASEQDIDTAMR 420
             +AT KA +Y QQQGK VLQIADYPG+L+WRTVAM++NEALDALQKGVAS +DIDTAMR
Sbjct: 359 SQAATDKATFYFQQQGKKVLQIADYPGLLVWRTVAMLVNEALDALQKGVASAEDIDTAMR 418

Query: 421 LGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEERYRPCSLLRQRALLESGYE 474
           LGVNYP GPLAWG  LGW R+LRLLENLQ HYGEERYRPCSLLRQ+AL+E  +E
Sbjct: 419 LGVNYPRGPLAWGESLGWGRVLRLLENLQRHYGEERYRPCSLLRQKALMEKHHE 472


Lambda     K      H
   0.319    0.134    0.386 

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: 645
Number of extensions: 18
Number of successful extensions: 4
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: 475
Length of database: 473
Length adjustment: 33
Effective length of query: 442
Effective length of database: 440
Effective search space:   194480
Effective search space used:   194480
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: 51 (24.3 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, or view the source code.

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