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 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