Alignments for a candidate for fadB in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Cereibacter sphaeroides ATCC 17029

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_011842152.1 RSPH17029_RS16015 enoyl-CoA hydratase/isomerase family protein

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



>NCBI__GCF_000015985.1:WP_011842152.1
          Length = 655

 Score =  499 bits (1285), Expect = e-145
 Identities = 292/653 (44%), Positives = 391/653 (59%), Gaps = 12/653 (1%)

Query: 8   DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67
           D++ R     + L+T+ + PVNAL   VR+ L A     +AD++V AV++   GR F+ G
Sbjct: 4   DLIRRSDFDGIALLTLANPPVNALGLAVRQRLTALTAELEADESVRAVVLTAEGRVFVGG 63

Query: 68  ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127
           ADI EF +PP  P LPDV   IEA  KP +AA++GAALGGG E+AL  HYRI  D A+LG
Sbjct: 64  ADIAEFDRPPEAPHLPDVIAAIEASRKPWIAALNGAALGGGAELALGCHYRIFADTARLG 123

Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187
           LPE  LGL+PGAGGTQR PR IG   A+++I +GR  SA EA   GL DR+ + + ++ E
Sbjct: 124 LPETSLGLIPGAGGTQRLPRRIGLAPAIEVITAGRTLSAAEAREAGLADRIAAGE-LIPE 182

Query: 188 GLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247
            LA+   L  A   + R   AA L+D     A    ARA  A+ +RG  +P   ++A+ A
Sbjct: 183 ALAFARTLDGA---LPRPASAAPLADPGH--AFWDEARARIARAARGNPAPTAALEAIRA 237

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVG 307
            + + F  GLR ER+ FL    S + A L H FFAER  L+    R  +P  L   GV+G
Sbjct: 238 GVAEGFAAGLRAERETFLRLRASDEAAALRHLFFAERAALRPAALRGIEPVPLTRAGVIG 297

Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367
           GGTMG+GIA A+  AGL V + E    +LA G   +E +++  + +G          M+R
Sbjct: 298 GGTMGSGIAAALAAAGLEVRLTETGPEALAAGLERVEAIFEAQVKRGLTDRAGATERMAR 357

Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427
            +G+    ALA  DLVIEAVFEDLAVK+ VF EL R+C   A+LATNTSYLD + +   +
Sbjct: 358 VTGTVGLGALADCDLVIEAVFEDLAVKRRVFEELVRLCGPEAILATNTSYLDPERIVEGL 417

Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487
             P   I LHFFSPA +MKLLE+V     +  ++AT   LA +L K PV+AG  +GFIGN
Sbjct: 418 PHPHRFIALHFFSPAQVMKLLEIVPLAATAPRILATGVALAARLGKIPVQAGNGEGFIGN 477

Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547
           R+L  YR+ A+A++  GA+P +ID A+RAFG  MGPF++ D+AG DI + AR+   A   
Sbjct: 478 RILKRYRAEAEALLLAGATPTEIDEAMRAFGLGMGPFEMQDMAGLDIAFRAREAARALGQ 537

Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607
                    DRL   G  G+KSG G+Y Y  GSR   P PE  A+I A     G  P   
Sbjct: 538 DLPE--GPGDRLVRAGRLGRKSGGGWYDYAPGSRLPQPSPEAAALI-APLVTPGARP--- 591

Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660
           +  EI  R +AAM  EG  +  E +A  P D+D+  ++GYGFPR++GGPM +A
Sbjct: 592 SGTEIADRLIAAMAEEGQRICDEGLAQSPSDIDLVEVHGYGFPRHKGGPMFHA 644


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: 1144
Number of extensions: 49
Number of successful extensions: 4
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: 655
Length adjustment: 39
Effective length of query: 667
Effective length of database: 616
Effective search space:   410872
Effective search space used:   410872
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 10 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
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