GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Neptunomonas antarctica S3-22

Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_054340851.1 Nant_RS06010 NAD(P)-dependent alcohol dehydrogenase

Query= BRENDA::Q8H0L8
         (359 letters)



>NCBI__GCF_001305295.1:WP_054340851.1
          Length = 349

 Score =  317 bits (811), Expect = 4e-91
 Identities = 164/348 (47%), Positives = 233/348 (66%), Gaps = 9/348 (2%)

Query: 16  WATRHTSGVLSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMVPGHEVV 75
           +A +  +  ++P N  RR      V   ++YCG+CHSD+HQ +N+WGN+ YP+VPGHE++
Sbjct: 5   YAAQTATSKMAPLNIQRRTLRPDDVAIDILYCGVCHSDIHQAENDWGNSIYPVVPGHEII 64

Query: 76  GVVIEVGSKVEKFKVGDKVGVGCMVGSCRKCENCTVDLENYCPR-QIPTYNGYS-LDGTL 133
           G V  +G  V ++KVGD VGVGCMV SC  C +C   LE YC    + TYNG    DGTL
Sbjct: 65  GRVTSIGPNVTQYKVGDIVGVGCMVDSCCSCSSCHAGLEQYCENGMVGTYNGKDYYDGTL 124

Query: 134 TFGGYSDMMVSDEHFVVRWPENLSMD-AAPLLCAGITTYSPLKYFGLDKPGMHIGVVGLG 192
           T GGYS+ +V  E FV+  P+ L +  AAPLLCAGITTYSPLK++G+ K G  +G++G+G
Sbjct: 125 TSGGYSEHIVVREAFVLSIPDTLDIKAAAPLLCAGITTYSPLKHYGV-KAGDKVGILGMG 183

Query: 193 GLGHMAVKFAKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAMNTLDGIID 252
           GLGHM VK+AKA G +VTV + S +K  EA + LGAD  ++S D +QM AA  T + ++D
Sbjct: 184 GLGHMGVKYAKALGAEVTVFTRSQSKVAEA-KLLGADHVIVSTDADQMAAATLTFNFLLD 242

Query: 253 TVSAVHPILPLLMLMKSHGKLVMVGAPEKPVELPVF--PLLMGRKLVAGSCIGGMKETQE 310
           T+   H   P L  +K  G  ++VG     ++ P++   L+  R+++AGS IGG+ ETQE
Sbjct: 243 TIPVAHDFNPYLNCLKVDGAHIIVGL-VTGIDPPIWGASLITKRRILAGSMIGGIAETQE 301

Query: 311 MLDFAAKHNITPDIEVVPMDYVNTALERLLKSDVKYRFVLDIGNTLNK 358
           ML+F+A+H I  ++E++ +  +N A ER+ K DVKYRFV+D+ N+L K
Sbjct: 302 MLNFSAEHGINCEVEMLDIQNINVAYERMKKGDVKYRFVIDM-NSLKK 348


Lambda     K      H
   0.320    0.137    0.417 

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: 342
Number of extensions: 19
Number of successful extensions: 6
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: 359
Length of database: 349
Length adjustment: 29
Effective length of query: 330
Effective length of database: 320
Effective search space:   105600
Effective search space used:   105600
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: 49 (23.5 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