GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Marinobacter adhaerens HP15

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  304 bits (779), Expect = 2e-87
 Identities = 165/318 (51%), Positives = 221/318 (69%), Gaps = 11/318 (3%)

Query: 1   MTGLLLKDIRKSYGAV--DVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58
           M+ L L+ IRK+Y  V  + + GID+DI  GEF++ VGPSGCGKSTL+  IAGLE IT G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118
            + +DG+ ++ + P  R IAMVFQSYALYP M+V +N+AFG++I    K EID+ V   A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178
           D+LQ++P +++ P  LSGGQ+QRVA+GRA+ R P+++LFDEPLSNLDA LRV  R EI K
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSP 238
           L +R+  TT++YVTHDQ+EAMTLADRI VL  G ++Q+G P E+Y+RP NLFVA F+GSP
Sbjct: 181 LHQRLK-TTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSP 239

Query: 239 AMNVIPATIT--ATGQQTAVSLAGGKSVTLDVPTNASEN-GKTASFGVRPEDLRVTEADD 295
           AM+ +P T+     G Q  V    G+SV L VP   ++  GK    G+RPE   +T+  D
Sbjct: 240 AMSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPE--HITQPQD 297

Query: 296 FLFEGTVSIVEALGEVTL 313
              + T   + A GE T+
Sbjct: 298 QKNDQT---LVAKGEFTI 312


Lambda     K      H
   0.320    0.137    0.387 

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: 372
Number of extensions: 15
Number of successful extensions: 2
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: 362
Length of database: 372
Length adjustment: 30
Effective length of query: 332
Effective length of database: 342
Effective search space:   113544
Effective search space used:   113544
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 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