GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Halococcus hamelinensis 100A6

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_007695653.1 C447_RS15655 ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_000336675.1:WP_007695653.1
          Length = 332

 Score =  125 bits (315), Expect = 9e-34
 Identities = 77/253 (30%), Positives = 134/253 (52%), Gaps = 24/253 (9%)

Query: 4   LEVQDLHKRY-GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62
           +   ++HK+Y      + G   +   G    ++G SG GK+T +R +N LE+P  G I  
Sbjct: 2   IRFDNVHKQYPDGTRAVDGHDFEVEEGTTTVLVGPSGCGKTTTMRLVNRLEEPTEGTIYY 61

Query: 63  NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122
           +  +++        L+A D      +R  +  V Q   L+ HMT  EN+   P  + G  
Sbjct: 62  DGTDIE-------ELEATD------LRREIGYVIQDIGLFDHMTVGENVATVP-ELKGWE 107

Query: 123 KTEAREKAEHYLNKVGVAHR--KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180
                ++ +  L  +G+     +D+YPG +SGG+QQRV +ARALA  P+VML DEP  AL
Sbjct: 108 AERTADRVDELLELMGLPPEEFRDSYPGELSGGQQQRVGVARALAAGPDVMLMDEPFGAL 167

Query: 181 DP----ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREV 236
           DP    EL  + L + + +     T+V VTH++  A ++ +++  +++G V +   P  +
Sbjct: 168 DPITREELQDEFLDIQKEI---DTTIVFVTHDINEALKMGDKIAVMNEGKVVQYDTPTAL 224

Query: 237 LVNPQSERLQQFL 249
           L NP+++ +++F+
Sbjct: 225 LDNPKTKFVEEFI 237


Lambda     K      H
   0.317    0.131    0.366 

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: 194
Number of extensions: 10
Number of successful extensions: 4
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: 254
Length of database: 332
Length adjustment: 26
Effective length of query: 228
Effective length of database: 306
Effective search space:    69768
Effective search space used:    69768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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