GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Flavobacterium beibuense F44-8

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate WP_035130886.1 Q763_RS02520 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_16275
         (244 letters)



>NCBI__GCF_000769915.1:WP_035130886.1
          Length = 222

 Score =  140 bits (353), Expect = 2e-38
 Identities = 85/221 (38%), Positives = 129/221 (58%), Gaps = 8/221 (3%)

Query: 1   MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEP--FQKG-D 57
           MI  KN++K+Y    VL      +KKGEV+ + G SG+GK+TL++ +  L+    +KG  
Sbjct: 1   MIQAKNIHKYYDSLHVLKGVDLHIKKGEVVSIVGASGAGKTTLLQILGTLDKPKSEKGTS 60

Query: 58  VVVDGTSIADPKTD-LPKLRS-RVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATK 115
           +++DG  + + K   L K R+ ++G +FQ  +LFP  T  EN+ I    + G+ K E   
Sbjct: 61  LLIDGEDVLNMKDKALSKFRNLKLGFIFQFHQLFPEFTALENVCIPAF-IAGKQKAETEA 119

Query: 116 KGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEV 175
           +  +LLE +GLS   +  PG+LSGG+QQRVA+ARAL   P V+  DEP+  LD      +
Sbjct: 120 EAKKLLEYLGLSHRINHKPGELSGGEQQRVAVARALINKPAVIFADEPSGNLDTHSAENL 179

Query: 176 LDVMVQLANE-GMTMMCVTHEMGFARKVADRVIFMDQGKII 215
            ++  +L +E G T + VTH    A  +ADR + M  G+II
Sbjct: 180 HNLFFKLRDEMGQTFVIVTHNEELA-NMADRKLVMSDGQII 219


Lambda     K      H
   0.321    0.136    0.394 

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: 126
Number of extensions: 9
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: 244
Length of database: 222
Length adjustment: 23
Effective length of query: 221
Effective length of database: 199
Effective search space:    43979
Effective search space used:    43979
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: 46 (22.3 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