Aligments for a candidate for fadB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadB in Phaeobacter inhibens BS107

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate GFF400 PGA1_c04110 putative fatty acid oxidation complex subunit alpha

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>lcl|FitnessBrowser__Phaeo:GFF400 PGA1_c04110 putative fatty acid
           oxidation complex subunit alpha
          Length = 697

 Score =  729 bits (1883), Expect = 0.0
 Identities = 389/701 (55%), Positives = 491/701 (70%), Gaps = 13/701 (1%)

Query: 8   DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67
           + +  E  G + ++   + PVNAL  DVRRGLLA IE A+ + A  AVLI G GR + AG
Sbjct: 3   EAIVYERIGDIAVLAAQNPPVNALGIDVRRGLLAGIERAEKEGA-RAVLIYGEGRTYFAG 61

Query: 68  ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127
           ADIREFGKP   P LPD+CNRIEA    VV+A+HG ALGGGLEVAL++HYRIAV GAK+G
Sbjct: 62  ADIREFGKPMEEPGLPDLCNRIEAAKLIVVSALHGTALGGGLEVALSSHYRIAVPGAKMG 121

Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187
           LPEV LG++PGAGGTQR PR+ G +AAL++I +GRH +A EA   G+IDR+   +     
Sbjct: 122 LPEVHLGIIPGAGGTQRLPRVAGTEAALEMITTGRHVAAAEAFDKGVIDRIAEGNP-REV 180

Query: 188 GLAYVHELLAAHAPVRRTRDAAALS--DRAASLAAVATARAETAKKSRGLFSPLKIVDAV 245
           GLAY  ELL  +AP R   D  A    D  A+   V         + RG  SP   V AV
Sbjct: 181 GLAYTRELLEQNAPRRPVCDMPAPEPVDFDATYERVLV-------RGRGQLSPAIAVRAV 233

Query: 246 EAAIEQP-FDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIG 304
           +AA E P F +G+R ER+LF++ ++S QR GLIHAFF+ER V K PE     PR +  +G
Sbjct: 234 QAACEAPSFLDGVRQERELFMKLMESDQRQGLIHAFFSERAVSKLPELVDVFPRDVAAMG 293

Query: 305 VVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAAL 364
           V+GGGTMGAGIA A L AGL V +IERD+A+    R  IE    G + +G++S  +  A+
Sbjct: 294 VIGGGTMGAGIATAALLAGLSVVLIERDEAASVAARERIEGNLRGALKRGKISQSQFDAI 353

Query: 365 MSRWSG-STSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDAL 423
           ++     +T Y AL+  DLV+EAVFED+ VK+ VFA LD  CK GA+LA+NTSYLDI+ +
Sbjct: 354 LNETLKLATDYAALSQVDLVVEAVFEDMDVKRDVFAALDEHCKPGAILASNTSYLDINDI 413

Query: 424 ASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDG 483
           A++ SRP+DVIGLHFFSPA++MKLLEVVV  Q + DVVAT F L K+L+KT VR+GVCDG
Sbjct: 414 AAATSRPSDVIGLHFFSPAHVMKLLEVVVADQTAPDVVATGFALGKRLKKTSVRSGVCDG 473

Query: 484 FIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRA 543
           FIGNR++  YR AAD M+ DGASPYQID  +  FGF MGPF V DLAG DIGWAARKRRA
Sbjct: 474 FIGNRIMNSYRKAADYMVLDGASPYQIDKVMTGFGFAMGPFAVADLAGLDIGWAARKRRA 533

Query: 544 ATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGIT 603
            T +P  R V  +D LCE G FGQK+GRGFY+Y EG R GTP+P+V   I+ ++   G+T
Sbjct: 534 PTLDPRERVVHFSDMLCEGGDFGQKTGRGFYVYEEGKRGGTPNPQVAEYIERDQRDQGVT 593

Query: 604 PRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMV 663
           P+ F ++E++RRYM AM+NE A VV E IA RPLDVD+  L+GYGFPR+ GGP+K+AD+ 
Sbjct: 594 PQIFANDEVLRRYMCAMVNEAAKVVGEGIARRPLDVDMVLLFGYGFPRFWGGPLKWADLQ 653

Query: 664 GLPKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQ 704
           G   IL DIR +AKED  FW+P+PLL ++V  G  F  LN+
Sbjct: 654 GPDSILKDIRRYAKEDAFFWQPAPLLEQMVAEGRSFDDLNK 694


Lambda     K      H
   0.320    0.136    0.392 

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: 1251
Number of extensions: 45
Number of successful extensions: 6
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: 706
Length of database: 697
Length adjustment: 39
Effective length of query: 667
Effective length of database: 658
Effective search space:   438886
Effective search space used:   438886
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: 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 preprint 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