GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  211 bits (536), Expect = 3e-59
 Identities = 125/346 (36%), Positives = 183/346 (52%), Gaps = 30/346 (8%)

Query: 1   MTALQLTNVCKSFG--PVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAG 58
           M+ +Q  NV K +       +  +NL + +GE +  +GPSGCGK+T LR+++G E  T G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 59  EISIGGQTV----TTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARV 114
           +I IG + V       PP KRGI MVFQ YAL+PHL++ +N+   L   R    +   R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118

Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174
            E   ++ L ++  R PSELSGGQ+QRVA+ RA+   PK+ L DEP SNLDA LR   R 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFI 234
           ++  + R+ +A+ I VTHDQ +A  ++D++VV+ +G I+Q+  P E+Y  PAN FVA+F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 235 G---------APAMNFV---------PAQRLGGNPGQFIGIRPEYARISPVGPLAGEVIH 276
           G          P +  V         P +         + IRPE  R++  G  AG V  
Sbjct: 239 GKTNLISGTLCPDLKHVETHIGRVCLPQETDKVIENVMVSIRPEGCRLAEKGRYAGLVER 298

Query: 277 VEKLGGDTNILVDMGEDLTFTARLF----GQHDTNVGETLQFDFDP 318
           V   G    + V +  D      +      + D  +G  + FD  P
Sbjct: 299 VTYSGEYQEVHVRLQSDQVSNDPMIIYAPIEQDIEIGSVVSFDITP 344


Lambda     K      H
   0.320    0.137    0.391 

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: 307
Number of extensions: 11
Number of successful extensions: 3
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: 331
Length of database: 351
Length adjustment: 28
Effective length of query: 303
Effective length of database: 323
Effective search space:    97869
Effective search space used:    97869
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