GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Acidovorax sp. GW101-3H11

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate Ac3H11_615 L-arabinolactonase (EC 3.1.1.15)

Query= BRENDA::Q15493
         (299 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_615
          Length = 316

 Score =  154 bits (390), Expect = 2e-42
 Identities = 93/283 (32%), Positives = 146/283 (51%), Gaps = 9/283 (3%)

Query: 6   IECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALR- 64
           + CV+      GE  +W     ++ +VDI  +++ RWD  T   QR T D  +S++A R 
Sbjct: 25  VRCVIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERA 84

Query: 65  QSGGYVATIGTKFCALNWKEQSAV-VLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETA 123
            + G++ T+   F   +     A   L   + D+  NRFNDGK D  GR++AG+M     
Sbjct: 85  HAPGFIVTLRRGFALFDPATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSM----- 139

Query: 124 PAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHK--IFYYIDSLSYSVDAFDYD 181
               E   GALY    D    ++ D   ++NG  WS   +    ++  ++  +   +D D
Sbjct: 140 DFACEAPTGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSD 199

Query: 182 LQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLP 241
           L TG +SN+        E+ +PDGM  DA+G+LW+A + G  V   DPVT   L  V+LP
Sbjct: 200 LATGTVSNKTLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLP 259

Query: 242 VDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKI 284
           V + T+C FGG +   ++++ AR G+ PE L  +P AG +F +
Sbjct: 260 VSQVTTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAV 302


Lambda     K      H
   0.319    0.136    0.421 

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: 315
Number of extensions: 17
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: 299
Length of database: 316
Length adjustment: 27
Effective length of query: 272
Effective length of database: 289
Effective search space:    78608
Effective search space used:    78608
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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