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_109940824.1 DLD82_RS09165 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_003173335.1:WP_109940824.1
          Length = 616

 Score =  431 bits (1108), Expect = e-125
 Identities = 236/538 (43%), Positives = 335/538 (62%), Gaps = 23/538 (4%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+  DV +    K+R +K A++W +   GEE   ++ ++S  SN +++ + K+ + KGD
Sbjct: 79  FNFGFDVVDAWAKKDR-NKIAMVWTN-QKGEEKFFTFRDISRRSNEIVNMMIKYKIGKGD 136

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V +M    P  W + +A+IK G + +P+ T LT  ++ YR +  +   +I+D   A  +
Sbjct: 137 RVLIMLHRVPEWWFMTVALIKIGAIYIPAPTMLTPKDIAYRVNTAEAKMVITDMENAHKV 196

Query: 158 EEALGSLK--VEKFLIDGKRETWNSLEDESSNAEP-----------EDTRGEDVIINYFT 204
           +E +G     V K ++DG+ + W S   E     P             T+  + ++ +F+
Sbjct: 197 DEIVGDCPTLVTKMVVDGECDGWLSYTRELMYPAPVSSRIINLKGMRKTKSSEPMVIFFS 256

Query: 205 SGTTGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVG 263
           SGTTG PK V H+  SYP+G I TA     VR +DLH  +S TGWAK AW   F   + G
Sbjct: 257 SGTTGEPKMVQHSH-SYPLGHIVTARFWHDVRNNDLHFTVSDTGWAKSAWGKLFGQWIEG 315

Query: 264 ATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGE 323
           A +   +Y  + +    L  +E  G+T+FCAPPT +R  I  DL ++ F  LR  VSAGE
Sbjct: 316 AAIFVYDYRSRFNATELLPLIEKYGITTFCAPPTIYRMLIMADLRKWDFSELRHCVSAGE 375

Query: 324 PLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEG 383
            +NPEVIK WKD   L I + YGQTET   VG FP ++ K GSMGKP P ++I L D++G
Sbjct: 376 LINPEVIKAWKDATGLEIYEGYGQTETVLCVGTFPCMEPKYGSMGKPSPGWEIELHDEDG 435

Query: 384 KEITKPYEVGHITVKLNPRPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFV 442
            ++ KP E G I +K  PRP+G F+ Y  +E+ N  SF+ GYYYTGD+A  D +GYF+FV
Sbjct: 436 NQV-KPGEEGSIAIKTEPRPVGFFMEYWGNEEANANSFKGGYYYTGDRAMKDNDGYFWFV 494

Query: 443 GRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSK 502
           GR DDVIK S YR+GPFEVESA++EHPAV EAAVVG PD +R  +VKA++VLK G+ PS+
Sbjct: 495 GRDDDVIKASGYRIGPFEVESAIIEHPAVQEAAVVGSPDIIRGFIVKAFVVLKAGFEPSE 554

Query: 503 ELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELR----KREEEKRKKGE 556
           +++ +I+E +K   +PYK PR IEF+ ELPKTISGKI+R +LR    KR E ++K G+
Sbjct: 555 KISRDIQEYVKNSTAPYKYPRKIEFIKELPKTISGKIKRKDLRELEMKRFEVEQKNGD 612


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: 852
Number of extensions: 40
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: 616
Length adjustment: 37
Effective length of query: 527
Effective length of database: 579
Effective search space:   305133
Effective search space used:   305133
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