GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Geotalea uraniireducens Rf4

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  221 bits (564), Expect = 2e-62
 Identities = 121/258 (46%), Positives = 168/258 (65%), Gaps = 9/258 (3%)

Query: 3   ELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTI 62
           EL + D+  + G   ++KGV LD+  GE V  +GPSG GK+TLLR IAGLE  S G + I
Sbjct: 5   ELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRI 64

Query: 63  ------DDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNE 116
                 +  +  +V   KR +  VFQSYAL+PH TV EN+ + L+   VP  EI +RV E
Sbjct: 65  GEQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQE 124

Query: 117 AAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEI 176
               L LG L +R P QLSGGQ+QRVA+ R++V +P++ L DEPLSNLDA+LR   RI +
Sbjct: 125 VLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWL 184

Query: 177 ARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGS 236
            +L   L  + V VTHDQ EAM +ADK+V+++ GV+EQ G+P ++Y  P +LFVA F+G+
Sbjct: 185 RQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGA 244

Query: 237 PKMNFLKGVI-EIDEDQA 253
              N + G++ ++D D A
Sbjct: 245 --NNTISGLVTDVDGDSA 260


Lambda     K      H
   0.321    0.139    0.396 

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: 347
Number of extensions: 16
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: 358
Length of database: 353
Length adjustment: 29
Effective length of query: 329
Effective length of database: 324
Effective search space:   106596
Effective search space used:   106596
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 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