GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Jannaschia aquimarina GSW-M26

Align Histidine transport system permease protein HisQ (characterized)
to candidate WP_043917275.1 jaqu_RS02045 ABC transporter permease subunit

Query= SwissProt::P0A2I9
         (228 letters)



>NCBI__GCF_000877395.1:WP_043917275.1
          Length = 237

 Score =  176 bits (445), Expect = 5e-49
 Identities = 93/219 (42%), Positives = 137/219 (62%)

Query: 4   GFSGVILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPDLV 63
           G+ G +L+G + TL++AL +  L + IG++GA  K+    +     E YTTLIR VP+LV
Sbjct: 14  GWGGNLLRGLVSTLQIALGAYALGMSIGILGALGKIHGGPILRGALEVYTTLIRAVPELV 73

Query: 64  LMLLIFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGH 123
           L+LL+FY  Q A+NV+  SLG +++ +D +  GI  +GF+ GAY TE FRGAF AV  G 
Sbjct: 74  LILLLFYAGQDAINVILTSLGFERVILDGLWVGIYVIGFVQGAYSTEVFRGAFGAVAPGQ 133

Query: 124 IEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKATQLA 183
           IEAA A G +  +   R++ P M+ +ALPG+ N W +  K TAL++++G+ ++   T+ A
Sbjct: 134 IEAARAIGMSRLKVQTRVVIPLMLPFALPGLANLWLITTKDTALLAVVGVSELALETRQA 193

Query: 184 GKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSVG 222
             +T   F F V  G +YL+ T VSN +   LERR   G
Sbjct: 194 AGATRAYFLFYVAAGCLYLLVTLVSNQIFAWLERRLRRG 232


Lambda     K      H
   0.328    0.144    0.422 

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: 169
Number of extensions: 8
Number of successful extensions: 1
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: 228
Length of database: 237
Length adjustment: 23
Effective length of query: 205
Effective length of database: 214
Effective search space:    43870
Effective search space used:    43870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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