GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Sphingomonas koreensis DSMZ 15582

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= uniprot:Q92L07
         (510 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  211 bits (538), Expect = 4e-59
 Identities = 151/468 (32%), Positives = 217/468 (46%), Gaps = 17/468 (3%)

Query: 25  KDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLL 84
           K L      P   P TG   A     S A+    +  A  AF  W   P   R   +  +
Sbjct: 11  KPLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAILAI 70

Query: 85  GEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHR 144
            + + A K +L RL+S E GK     +GE+   +       GL      + +  +    R
Sbjct: 71  ADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRP---AVDVLKDDDSVR 127

Query: 145 MMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERA 204
           +     PLGVV  IS +NFPV +  W+    LV G+ VV KPS  TPL AL    I    
Sbjct: 128 VEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIANAH 187

Query: 205 IARFGDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILE 264
           +      P G+   + G+  IG  +  HP +  +  TGST  GR +    A    R  LE
Sbjct: 188 L------PPGVLNSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLE 241

Query: 265 LGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQS 324
           LGGN+A IV P AD+D     I   A G +GQ C  ++R++VHES++D L  +L +  ++
Sbjct: 242 LGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMART 301

Query: 325 VSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALV 384
             VG   ++A+  GP+ ++  FD ++    +A+ HGG    G     G  +GY+  P  V
Sbjct: 302 AVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREG--DGYFF-PLSV 358

Query: 385 EMPKQEGP--VLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAA 442
            +   +G   V EE F PIL V++YSD +  LA  NA   GL  S+++ D   +  F  A
Sbjct: 359 VVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAF--A 416

Query: 443 DGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRAT 490
              + G   VN   S       FGG K++G G E G    + YM+  T
Sbjct: 417 QRLEAGTVWVNDHAS-ISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQT 463


Lambda     K      H
   0.317    0.134    0.390 

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: 577
Number of extensions: 25
Number of successful extensions: 3
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: 510
Length of database: 469
Length adjustment: 34
Effective length of query: 476
Effective length of database: 435
Effective search space:   207060
Effective search space used:   207060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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