GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Methanococcus aeolicus Nankai-3

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_011974130.1 MAEO_RS07290 ATP-binding cassette domain-containing protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_000017185.1:WP_011974130.1
          Length = 373

 Score =  157 bits (396), Expect = 6e-43
 Identities = 102/304 (33%), Positives = 169/304 (55%), Gaps = 22/304 (7%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           LE++N+ K        TL+   L+IK+ ++ I +G SG GK+TL+  +AG      G I+
Sbjct: 2   LEIKNLKKKLN---DFTLEIDNLTIKDDDYFIFLGLSGSGKTTLLEIMAGFSKADSGTIL 58

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           +  +D++      R+IA+    Y L+P +++ +NIE G+K        I+  +  +AK L
Sbjct: 59  LDGKDITNKPINKRNIALCNGKY-LFPHLTISKNIELGIKNNSNKNDKIEI-IENIAKTL 116

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK-LMH 182
           +I+HLLNR P  LS G++QRV++  ALA  P+I L DEPLS+LD  +  E+  E++ + H
Sbjct: 117 KIKHLLNRYPKNLSMGERQRVSLAMALAMEPRIILLDEPLSSLDRLIHEELLYELREIYH 176

Query: 183 QRLKTTT--VYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
               TTT  ++VTHD  EA+ L + +A++  G I+Q G  KEI   P ++FVA F G   
Sbjct: 177 NSNNTTTTIIHVTHDFNEAIALSNNIAILNKGKIEQMGNIKEILRYPKSEFVAKFTGL-- 234

Query: 241 MNFVPLRLQR-----------KDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPE 289
            N +  R+ +           K+  +   L+    R    ++ ++  +  +  +LG+RPE
Sbjct: 235 RNLLNGRVIKQLNENEEIYLFKNENITIQLNGNDKRITKFIDNSKNQIY-KKALLGVRPE 293

Query: 290 QIML 293
           +IM+
Sbjct: 294 EIMI 297


Lambda     K      H
   0.318    0.135    0.382 

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: 290
Number of extensions: 15
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: 386
Length of database: 373
Length adjustment: 30
Effective length of query: 356
Effective length of database: 343
Effective search space:   122108
Effective search space used:   122108
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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