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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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