Aligments for a candidate for fadB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Aligments 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:

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 paper from 2022 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