GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Pantoea rwandensis LMG 26275

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_084933742.1 HA51_RS07075 urea ABC transporter permease subunit UrtB

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>NCBI__GCF_002095475.1:WP_084933742.1
          Length = 521

 Score =  121 bits (304), Expect = 3e-32
 Identities = 86/288 (29%), Positives = 143/288 (49%), Gaps = 5/288 (1%)

Query: 7   QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWVP 66
           Q   GLSLG+I  L A+G  + YG++G+IN AHGE+ M+GA+               W+ 
Sbjct: 228 QAFTGLSLGSILLLAALGLAITYGLLGVINMAHGEMLMLGAYATWFVQNLFQQFAPQWLA 287

Query: 67  LALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGARS 126
              L+ L  + L TA  G  +ER   R L   P L  L++  G+S+ L   V++L GA++
Sbjct: 288 WYPLLALPVAFLVTAGIGMLLERTIIRHLYGRP-LETLLATWGISLMLIQLVRMLFGAQN 346

Query: 127 KPL--QPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDK 184
             +     L G   ++   V + Y R+A I+   A++     L+ +T LG + RA  Q++
Sbjct: 347 LEVANPSWLSGGWQVLPNLV-LPYNRIAVILFVFAVLGLTWLLLNKTRLGLSVRAVTQNR 405

Query: 185 KMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGI 244
            MA   GV   R+  L F +G+ +A + G + L   G +   +G    + +F   VLGG+
Sbjct: 406 AMADCCGVPTGRIDMLAFGLGSGIAGLGG-VALSQLGNVGPELGQGYIIDSFLVVVLGGV 464

Query: 245 GSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292
           G L G ++    +G++       +G+    +    +++L +  RP GL
Sbjct: 465 GQLAGTVVAAFGLGILNKVLEPQIGAVLGKILILVLIILFIQKRPQGL 512


Lambda     K      H
   0.329    0.144    0.425 

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: 359
Number of extensions: 24
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: 301
Length of database: 521
Length adjustment: 31
Effective length of query: 270
Effective length of database: 490
Effective search space:   132300
Effective search space used:   132300
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 (21.8 bits)
S2: 50 (23.9 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