GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Geotalea uraniireducens Rf4

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

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  223 bits (569), Expect = 5e-63
 Identities = 145/345 (42%), Positives = 206/345 (59%), Gaps = 21/345 (6%)

Query: 18  IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDI------TEVS 71
           I+KG+ L+VN  E V  +GPSG GK+TLLR IAGLE  S G+I +  + +       EVS
Sbjct: 20  ILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKKIEVS 79

Query: 72  PAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKP 131
             KR L  VFQ+YAL+PH +V +N+++ L L  V   E+ ++V E    L LG + ER P
Sbjct: 80  VEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLSERHP 139

Query: 132 KQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQATMIYVT 191
            QLSGGQ+QRVA+ R++V NP++ L DEPLSNLDA LR + R+ L +L  +L  + + VT
Sbjct: 140 HQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSAVCVT 199

Query: 192 HDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLKGKITRVDS 251
           HDQ EAM MADKVV+L  G IEQ G+P ++Y  P +LFVA F+G      + G +T VD 
Sbjct: 200 HDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGANNT--ISGLVTDVDG 257

Query: 252 QGCEVQLDAGTRVSLPLGGR---HLSVGSAVTLGIRPEHLELAK-PGDCALQVTADVSER 307
               ++ +        L GR    L  G   T  +R E ++LA+ P + +L++    S  
Sbjct: 258 DSARIEGNGWA-----LRGRLRTPLKAGDRATAVVRLEKIKLAQTPKENSLRLPLTASVY 312

Query: 308 LGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLF 352
           LG +T+ +V   +G   T+R  G+   + GE L + + A+H  LF
Sbjct: 313 LG-NTWEYVFDLAG--ATIRGYGNEFMQPGEQL-VDIPAEHLWLF 353


Lambda     K      H
   0.320    0.137    0.389 

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: 310
Number of extensions: 12
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: 367
Length of database: 353
Length adjustment: 29
Effective length of query: 338
Effective length of database: 324
Effective search space:   109512
Effective search space used:   109512
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