GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt1d in Marinobacter adhaerens HP15

Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate GFF1055 HP15_1034 Zn-dependent alcohol dehydrogenase

Query= BRENDA::Q38707
         (365 letters)



>FitnessBrowser__Marino:GFF1055
          Length = 352

 Score =  320 bits (819), Expect = 5e-92
 Identities = 166/346 (47%), Positives = 236/346 (68%), Gaps = 9/346 (2%)

Query: 12  KAFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPG 71
           KAF  AA+  T  ++P    RR     DV +++ +CGVCH+D H   N+WG T YP+VPG
Sbjct: 6   KAF--AAQSPTSGMAPHTIDRRDPRPDDVAIEIDYCGVCHTDIHFAQNDWGITEYPVVPG 63

Query: 72  HEIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHC-ENTIDTY-GSIYF 129
           HEIVG VT VG +V+   VGD VG+GC+V SCR+C +C    E +C E    TY G    
Sbjct: 64  HEIVGRVTAVGPEVKSFNVGDVVGVGCMVDSCRTCSACEAGLEQYCSEGMTSTYNGQDRH 123

Query: 130 DGTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGV 189
           D ++T GGYS+ +   E F++R P+ L + + APLLCAGITTYSPL++YG+ K G K+GV
Sbjct: 124 DHSITFGGYSERITVSERFVVRIPEKLDIKAAAPLLCAGITTYSPLRHYGV-KAGHKVGV 182

Query: 190 VGLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLD 249
           +G+GGLGH+ VK A+A GA+VT+   SESK  EA +K GAD  ++++D++QM  A  + D
Sbjct: 183 IGMGGLGHMGVKFARALGAEVTIFTRSESKVPEA-KKQGADHVVISTDEDQMAAAAENFD 241

Query: 250 GIIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPV--FSLLKGRKLLGGTINGGIK 307
            ++DTVPV H L P  + LK +G  ++VG  E P E PV   +L+  R++L G++ GG+ 
Sbjct: 242 FMLDTVPVQHDLNPYLNCLKHDGTHILVGLLE-PVEPPVEAGALVFKRRVLAGSLIGGMP 300

Query: 308 ETQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDI 353
           ETQE+LDF A+H+++ DVE++ ++ +N A ER+ K DV+YRFVID+
Sbjct: 301 ETQEVLDFCAEHDVSCDVEMLDINNLNEAYERMKKGDVKYRFVIDM 346


Lambda     K      H
   0.319    0.137    0.415 

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: 368
Number of extensions: 13
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: 365
Length of database: 352
Length adjustment: 29
Effective length of query: 336
Effective length of database: 323
Effective search space:   108528
Effective search space used:   108528
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: 49 (23.5 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:

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