Aligments for a candidate for ech in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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:

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