GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella loihica PV-4

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__PV4:5210423
          Length = 708

 Score =  172 bits (436), Expect = 5e-47
 Identities = 133/409 (32%), Positives = 202/409 (49%), Gaps = 41/409 (10%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           KV VIGSG MG GIA      G    + D++ E L++ +  I+ +     + G L +  +
Sbjct: 301 KVAVIGSGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQAQL 360

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           ++ +A +   TD A  +   D VIEAV E +E+K+ +F+  +A   P A+LATNTS+L +
Sbjct: 361 DERMALLSGTTDYAD-IADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLDV 419

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
            EIA+    PQ V+G+HFF+P  +M L+EIVR   T+ + + TT ++A+ + K  +V   
Sbjct: 420 DEIAAETSRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSGV 479

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GF  NR     +     L+ +G AS  ++D     E G PMG+  + D  G+D+G   
Sbjct: 480 CWGFIGNRATDSYLRESMSLILEG-ASPAQID-KVHTEFGMPMGLPSMVDLAGIDVG--- 534

Query: 241 WKAVTARGFKAFPC-------SSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTL----P 289
              +T    KAF         +   KL ++ + G K+G G Y Y    K   P +     
Sbjct: 535 --ILTREDRKAFTTDLDPSHFAILHKLYAKQRYGQKTGRGLYIYEGRDKQEDPEVLELAA 592

Query: 290 STSKKLG---------------RYLISPAVNEVSYLLREGI-VGKDDAEKGCVLGLGLP- 332
             +K+ G                  I P +NE + +L EGI +   D +     G G P 
Sbjct: 593 EAAKEFGVTRRSPEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPI 652

Query: 333 --KGILSYADEIGIDVVVNTLEEMRQT--SGMDHYSPDPLLLSMVKEGK 377
              G + YADEIG++ V+  L + R T   G   + P PLL  +VKEGK
Sbjct: 653 FRGGPMQYADEIGLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGK 701



 Score =  107 bits (268), Expect = 1e-27
 Identities = 62/167 (37%), Positives = 96/167 (57%), Gaps = 6/167 (3%)

Query: 408 AWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT 467
           A I+LN+P   N++   +   +   L   E  E V  I +   G++F  GAD++EF S  
Sbjct: 14  AVIILNQPP-VNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISEFSS-- 70

Query: 468 PVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEI 527
                +A     +V   ++   K V+A +NGLALGGG EL L+ D+R+A   A++G PE+
Sbjct: 71  --DDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPEV 128

Query: 528 NLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFL 573
           NLG++PG GGTQRL R+ G +  LE++ +GR + A      G+++ L
Sbjct: 129 NLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNL 175


Lambda     K      H
   0.316    0.134    0.377 

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: 928
Number of extensions: 56
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 708
Length adjustment: 39
Effective length of query: 612
Effective length of database: 669
Effective search space:   409428
Effective search space used:   409428
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 (21.6 bits)
S2: 54 (25.4 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