GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF400
          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:

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