GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Phaeobacter inhibens BS107

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 GFF2242 PGA1_c22740 fatty acid oxidation complex subunit alpha

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Phaeo:GFF2242
          Length = 706

 Score =  175 bits (444), Expect = 5e-48
 Identities = 123/398 (30%), Positives = 195/398 (48%), Gaps = 26/398 (6%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62
           V VIG+G MG GIA     AG  V + + +   L+Q +E+++    +  + G L     +
Sbjct: 297 VAVIGAGTMGRGIAIAFLQAGYPVTLLETTQGALEQGLEKVREHFQRAAQKGRLSADRAE 356

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
            ++     T     L  +D +IEA  E + +KR IF   + HA P A+LA+NTS+L + E
Sbjct: 357 AISANATGTLSYAGLAKADLIIEAAFESMNVKRQIFEALDLHAKPGAILASNTSTLDLDE 416

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           IA+V   P+ V+G+HFF+P  +M L+E+VRG  T+ +V+ T   +AK + K  + V    
Sbjct: 417 IATVTSRPEDVIGLHFFSPANVMRLLEVVRGAKTAPDVIATAITVAKKIRKLPVTVGVCY 476

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GF  NR+L      G  L+ +G A+ ++VD   +E  G  MG+  +AD  G+D+G  V +
Sbjct: 477 GFVGNRMLEPYFREGSRLLLEG-ATPKQVD-DVLEGFGMAMGIHAMADLAGVDVGARVRQ 534

Query: 243 AVTAR-GFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTSKKLG----- 296
              +         +  ++L   G+LG K+G G Y Y    +   P +   S +L      
Sbjct: 535 ERRSEIAHDPTYQAVQDRLFELGRLGQKTGRGSYVYEGRTRVEDPEMVQISSELADLHGV 594

Query: 297 -----------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLPK---GILSYADE 341
                         + P +NE   +L EGI  +  D +   V G G P    G + YADE
Sbjct: 595 KRRDIDDQEILERCLFPLINEGFLILEEGIATRPGDCDLIWVNGYGFPNWRGGPMHYADE 654

Query: 342 IGIDVVVNTLEEMRQTSGM---DHYSPDPLLLSMVKEG 376
           IG+  ++  +   RQ+ G      ++P PLL  +   G
Sbjct: 655 IGLSQIMERMTHYRQSLGAYGEMWFTPAPLLEQLATSG 692



 Score =  110 bits (274), Expect = 3e-28
 Identities = 66/173 (38%), Positives = 103/173 (59%), Gaps = 6/173 (3%)

Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466
           +A+I LN P+  NA+   M + ++ A+  L+  E V+ I +     +F  GAD+ EF + 
Sbjct: 10  VAFIELNAPS-VNALGLKMRQVLSSAIHELDADEQVKAIVLCSALPLFCGGADIVEFRT- 67

Query: 467 TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPE 526
               A+       ++ + I+   KP+IA I G A+GG +E+AL+ D+RVA+  A MG PE
Sbjct: 68  ---GAVWDKPDLPDLCVMIETSKKPIIAAIAGPAMGGALEIALACDYRVATPDAVMGLPE 124

Query: 527 INLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEE 578
           I LGL+PG GGTQRL R++G     +++L+G  VK E A   G+V+ L E ++
Sbjct: 125 IKLGLLPGAGGTQRLPRIAGLEAATQMILSGDPVKGEYALSCGLVDALFENDQ 177



 Score = 40.0 bits (92), Expect = 4e-07
 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 7/116 (6%)

Query: 295 LGRYLISPAVNEVSYLLREGIVGK--DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLE 352
           +G  ++ P   E S LL EG   K  DD  +G     G+  GI + AD  G+DV     +
Sbjct: 479 VGNRMLEPYFREGSRLLLEGATPKQVDDVLEG----FGMAMGIHAMADLAGVDVGARVRQ 534

Query: 353 EMRQTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTIVVRVEPPLA 408
           E R     D  +   +   + + G+LG+K+G+G + Y          +V++   LA
Sbjct: 535 ERRSEIAHDP-TYQAVQDRLFELGRLGQKTGRGSYVYEGRTRVEDPEMVQISSELA 589


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: 971
Number of extensions: 47
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 706
Length adjustment: 39
Effective length of query: 612
Effective length of database: 667
Effective search space:   408204
Effective search space used:   408204
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