GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Methanospirillum stamsii Pt1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_109940443.1 DLD82_RS07265 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_003173335.1:WP_109940443.1
          Length = 555

 Score =  441 bits (1134), Expect = e-128
 Identities = 244/533 (45%), Positives = 331/533 (62%), Gaps = 21/533 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+  DV +     +R +K A+IW    TGEE K ++ +L  +S    + L K+G+KKGD
Sbjct: 27  FNFGFDVIDKWSETDR-NKLAMIWVS-QTGEEKKYTFRDLRNLSVEAANILLKYGVKKGD 84

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V LM    P  W   +A+IK G +  P+ T LT  +++YR +  K S II+D+  A  +
Sbjct: 85  RVMLMLHRIPEWWIFVIALIKLGAIFCPAPTMLTPKDLQYRVNAGKFSFIITDTENAEKV 144

Query: 158 EEALG---SLKVEKFLIDGKRETWNSLEDESSNAEPED-----------TRGEDVIINYF 203
           E+      S+K  + L+DG+   W S + E     P             T   D ++ YF
Sbjct: 145 EKICRFCPSIK-HRMLVDGQLPNWISFQYELFYPAPVSRSAISMPVSMKTHATDPMLIYF 203

Query: 204 TSGTTGMPKRVIHTAVSYPVGSITTASI-VGVRESDLHLNLSATGWAKFAWSSFFSPLLV 262
           TSGTTG PK V+H    +P+G I TA +   +  +DLH   S TGWAK  W   F   +V
Sbjct: 204 TSGTTGEPKMVLHDH-GHPLGHIVTARLWQDLNSNDLHFTSSDTGWAKCGWGKIFGQWIV 262

Query: 263 GATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAG 322
           GA +   +  GK      L  +E   + +FC PPT +R  I  DL ++    LR  +SAG
Sbjct: 263 GACIFIYDARGKFKATELLPLIEKYEINTFCCPPTVYRMLIIADLAKYDLRSLRHCISAG 322

Query: 323 EPLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDE 382
           EPLNPEVI+IWK++  L I + YGQ+ET   +  FP +K KPGSMGKP P + I L D+E
Sbjct: 323 EPLNPEVIRIWKEETGLPIYEGYGQSETCCCIATFPCMKHKPGSMGKPSPGWKIELHDEE 382

Query: 383 GKEITKPYEVGHITVKLNPRPIGLFLGYSDEKK-NMESFREGYYYTGDKAYFDEEGYFYF 441
           GK + +  E G I + LNPRP+GL + Y D  + N E F++G+YYTGDKAY DEEGYF+F
Sbjct: 383 GKPVPQGTE-GRIAISLNPRPVGLVVEYLDNPEANAEVFKDGFYYTGDKAYMDEEGYFWF 441

Query: 442 VGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPS 501
           VGR DDVIK+S YR+GPFEVESAL EHPAV E+AVVG PD +R  ++KA+++LK GY PS
Sbjct: 442 VGRDDDVIKSSGYRIGPFEVESALQEHPAVQESAVVGSPDPIRGLIIKAFVILKSGYEPS 501

Query: 502 KELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKK 554
           ++L  +I++ +K + +PYK PRIIEFVDELPKT+SGKI+R ELR+RE  K K+
Sbjct: 502 EQLIRDIQKHVKKVTAPYKYPRIIEFVDELPKTLSGKIKRAELRERELRKYKE 554


Lambda     K      H
   0.318    0.137    0.402 

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: 821
Number of extensions: 38
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: 564
Length of database: 555
Length adjustment: 36
Effective length of query: 528
Effective length of database: 519
Effective search space:   274032
Effective search space used:   274032
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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