GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Korea:Ga0059261_0837
          Length = 676

 Score =  562 bits (1449), Expect = e-164
 Identities = 316/691 (45%), Positives = 427/691 (61%), Gaps = 22/691 (3%)

Query: 10  VSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGAD 69
           ++ E +G +L++T ++ PVNAL A VR+GL AAI+    D +++A +I   GR F AGAD
Sbjct: 5   ITTERQGDILVITSNNPPVNALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFFAGAD 64

Query: 70  IREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLP 129
           I EFGKP   PSLP + + IEA  KPVVAA+HG ALGGG EVALA HYRIAV  AK GLP
Sbjct: 65  ITEFGKPMQEPSLPVLVDLIEASEKPVVAAVHGTALGGGCEVALACHYRIAVPSAKFGLP 124

Query: 130 EVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGL 189
           EV+LG+LPGAGGTQR PR+ G + AL+L   G   SA  A   GL+DRL   D + A+ +
Sbjct: 125 EVKLGILPGAGGTQRLPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAGEDSLTADAI 184

Query: 190 AYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAI 249
           AY +E+ AA  P+ RT +     +     A     R   AK+ R + +P +I+  +E   
Sbjct: 185 AYANEIAAAR-PLPRTSEKPVTVEAGVFEAF----RKTNAKRFRNMDAPAEIIAVIEETA 239

Query: 250 EQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPET-RAAKPRTLNTIGVVGG 308
            +P+ EG++ ER  F++ I   Q A L H FFAER+  K  +     K R +  +GV+G 
Sbjct: 240 GKPYAEGVQRERMGFMKLIMGAQSAALRHIFFAERKAAKIDDVPEDTKLRPIKRVGVIGA 299

Query: 309 GTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRW 368
           GTMG GI++  L AG+PVT+ E    +L RG   I K Y+   AKGR++AE+    M   
Sbjct: 300 GTMGGGISMNFLSAGIPVTIAEMQQEALDRGTGTIRKNYEATAAKGRMTAEQVEGAMGLL 359

Query: 369 SGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVS 428
             +   + LA  DL+IEAV+E++ VK+ +F +LD++ K GA+LA+NTSYL ID +AS+  
Sbjct: 360 KSTLDLNDLAECDLIIEAVYENMDVKKDIFGKLDKIAKPGAILASNTSYLSIDEIASATG 419

Query: 429 RPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNR 488
           RP DV+G+HFFSPANIMKLLEVV   +   DV+AT  +LAKK++K  V AGVC GFIGNR
Sbjct: 420 RPGDVVGMHFFSPANIMKLLEVVRGAKTDKDVLATVMDLAKKIKKVAVVAGVCYGFIGNR 479

Query: 489 VLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNP 548
           +L   +  A  ++ +GA+P Q+D     FG PMGPFQ+ DLAG DIGW         R+P
Sbjct: 480 MLIPRQMEAMKLLHEGATPMQVDKVHVEFGMPMGPFQMSDLAGVDIGW--------HRDP 531

Query: 549 AARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFT 608
             R   I D L     +GQK+  GFY Y +  R+ +P P V  II+  R + G      T
Sbjct: 532 -TRIENIRDALAAENRWGQKTKAGFYDY-DDKRNPSPSPRVAEIIEEFRTKTGTPQHEVT 589

Query: 609 DEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKI 668
           DEEI+ R    M+NEGA ++ E +A R  D+DV ++YGYG+P YRGGPM +AD VGL  I
Sbjct: 590 DEEIMERTFYTMVNEGAKILEEGMAQRASDIDVVWIYGYGWPPYRGGPMFWADQVGLKTI 649

Query: 669 LADIREFAKEDPLFWKPSPLLIELVERGADF 699
           +A + +        ++ S LL +  E G  F
Sbjct: 650 VAGLEKHG------FEISKLLRDKAESGGKF 674


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: 1110
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: 676
Length adjustment: 39
Effective length of query: 667
Effective length of database: 637
Effective search space:   424879
Effective search space used:   424879
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