Alignments for a candidate for fadB in Phaeobacter inhibens BS107

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 GFF2242 PGA1_c22740 fatty acid oxidation complex subunit alpha

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



>FitnessBrowser__Phaeo:GFF2242
          Length = 706

 Score =  514 bits (1323), Expect = e-150
 Identities = 297/688 (43%), Positives = 412/688 (59%), Gaps = 14/688 (2%)

Query: 18  VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77
           V  + ++   VNAL   +R+ L +AI   DAD+ V+A+++  A   F  GADI EF    
Sbjct: 10  VAFIELNAPSVNALGLKMRQVLSSAIHELDADEQVKAIVLCSALPLFCGGADIVEFRTGA 69

Query: 78  V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135
           V   P LPD+C  IE   KP++AAI G A+GG LE+ALA  YR+A   A +GLPE++LGL
Sbjct: 70  VWDKPDLPDLCVMIETSKKPIIAAIAGPAMGGALEIALACDYRVATPDAVMGLPEIKLGL 129

Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSD-DILAEGLAYVHE 194
           LPGAGGTQR PR+ G +AA  +ILSG     + AL+ GL+D L  +D D  A  L +   
Sbjct: 130 LPGAGGTQRLPRIAGLEAATQMILSGDPVKGEYALSCGLVDALFENDQDFRAHVLGFATR 189

Query: 195 LLAAHAPVRRTRDAAALSDRAASLAAVATA-RAETAKKSRGLFSPLKIVDAVEAAIEQPF 253
           +     P R   D   ++ R        T  R + A  S+ L +P + + ++EAA E P 
Sbjct: 190 VSHEGDPKRSCAD---MTVRHPDPKGYLTGFRDQIAHTSKNLVAPERCLVSIEAACEMPL 246

Query: 254 DEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPE-TRAAKPRTLNTIGVVGGGTMG 312
            EGL  E+  F E +D+PQ     H FFAERE  K P  TRA +PR + ++ V+G GTMG
Sbjct: 247 AEGLEQEKAGFAELLDTPQSRAGRHLFFAERECTKVPGVTRADRPRDIASVAVIGAGTMG 306

Query: 313 AGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGST 372
            GIA+A L AG PVT++E    +L +G   + + +     KGRLSA++  A+ +  +G+ 
Sbjct: 307 RGIAIAFLQAGYPVTLLETTQGALEQGLEKVREHFQRAAQKGRLSADRAEAISANATGTL 366

Query: 373 SYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPAD 432
           SY  LA ADL+IEA FE + VK+ +F  LD   K GA+LA+NTS LD+D +A+  SRP D
Sbjct: 367 SYAGLAKADLIIEAAFESMNVKRQIFEALDLHAKPGAILASNTSTLDLDEIATVTSRPED 426

Query: 433 VIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAV 492
           VIGLHFFSPAN+M+LLEVV   + + DV+ATA  +AKK+RK PV  GVC GF+GNR+L  
Sbjct: 427 VIGLHFFSPANVMRLLEVVRGAKTAPDVIATAITVAKKIRKLPVTVGVCYGFVGNRMLEP 486

Query: 493 YRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARY 552
           Y      ++ +GA+P Q+D  +  FG  MG   + DLAG D+G   R+ R +       Y
Sbjct: 487 YFREGSRLLLEGATPKQVDDVLEGFGMAMGIHAMADLAGVDVGARVRQERRSEIAHDPTY 546

Query: 553 VQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEI 612
             + DRL E G  GQK+GRG Y+Y EG R+   DPE+  I        G+  R   D+EI
Sbjct: 547 QAVQDRLFELGRLGQKTGRGSYVY-EG-RTRVEDPEMVQISSELADLHGVKRRDIDDQEI 604

Query: 613 IRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADI 672
           + R +  +INEG  ++ E IA RP D D+ ++ GYGFP +RGGPM YAD +GL +I+  +
Sbjct: 605 LERCLFPLINEGFLILEEGIATRPGDCDLIWVNGYGFPNWRGGPMHYADEIGLSQIMERM 664

Query: 673 REFAKE----DPLFWKPSPLLIELVERG 696
             + +       +++ P+PLL +L   G
Sbjct: 665 THYRQSLGAYGEMWFTPAPLLEQLATSG 692


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: 1120
Number of extensions: 44
Number of successful extensions: 5
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: 706
Length adjustment: 39
Effective length of query: 667
Effective length of database: 667
Effective search space:   444889
Effective search space used:   444889
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 Apr 09 2024. 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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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