GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  120 bits (300), Expect = 7e-32
 Identities = 87/291 (29%), Positives = 142/291 (48%), Gaps = 14/291 (4%)

Query: 27  LKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGK------VLFDGRDVTRASPQER 80
           L +E  +G    LLGPSGCGKTT L +++G   P+ GK      V++D R      P++R
Sbjct: 24  LNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIRIGDEVVYDDRRAL--PPEKR 81

Query: 81  NIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLA 140
            I  VFQ   ++  +T+ +N+ F L   K  +   K+R   + E++ +    ++  + L+
Sbjct: 82  GIGMVFQDYALFPHLTIEKNVTFGLNRWKNRDK--KKRAQEVLELVGLGEFGHRLPSELS 139

Query: 141 ADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQ 200
              +Q+++L R L       +L DEP + +D  L+ ++R  +  I  +   T I VTHDQ
Sbjct: 140 GGQQQRVALARALAPRP-KVILMDEPFSNLDAGLREKMRYDVTNILRKANATAIIVTHDQ 198

Query: 201 VEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVA 260
            +A   +D+VVVM  G   Q+ +   ++  PA+ FV  F+G   +       D +++   
Sbjct: 199 KDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFVGKTNLISGTLCPDLKHVETH 258

Query: 261 GHRLASPVGRALPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQ 311
             R+  P         + V IRPE   LA   + G   G V +V   G YQ
Sbjct: 259 IGRVCLPQETDKVIENVMVSIRPEGCRLA---EKGRYAGLVERVTYSGEYQ 306


Lambda     K      H
   0.320    0.136    0.395 

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: 266
Number of extensions: 7
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: 351
Length adjustment: 29
Effective length of query: 329
Effective length of database: 322
Effective search space:   105938
Effective search space used:   105938
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