GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Polaromonas naphthalenivorans CJ2

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease

Query= reanno::psRCH2:GFF851
         (296 letters)



>NCBI__GCF_000015505.1:WP_011803054.1
          Length = 289

 Score =  105 bits (261), Expect = 2e-27
 Identities = 84/287 (29%), Positives = 136/287 (47%), Gaps = 21/287 (7%)

Query: 17  HAALLAFVAAILFPLLMVISISFREGN-FATGSLF--PENPTLEHWSLALGIPYTHADGS 73
           +A LL      L P  ++++ SF++     +G+L   P +   + W LA     T  D  
Sbjct: 17  YAVLLVAALFFLAPFYVMLATSFKDAEQIRSGNLLSPPASLNFDAWRLAWSSACTGVDCR 76

Query: 74  VTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPP 133
             QP F      WNSV +A  + ++       + Y  +  +F G + +L   L+F +F P
Sbjct: 77  GLQPYF------WNSVSMAIPAVLISTAWGAVNGYVLSLWKFRG-SELLFGFLLFGVFMP 129

Query: 134 VLSLVAIYALFDQLGQHVSWLGVNSH--GAVIVASLGGMALHIWTIKGYFESIDASLEEA 191
              ++        + Q + +LG++S   G V+V  L GMA      + Y+ +I   L  A
Sbjct: 130 FQVVLL------PMSQVLGYLGLSSSIGGLVLVHCLAGMAGTTLFFRNYYTAIPKELVNA 183

Query: 192 AIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQ 251
           A +DGA  W+ F+ I+LP+S PIL V  I  F T++    +  V     D   ++VG   
Sbjct: 184 ARMDGAGFWRIFWRIVLPLSTPILMVTLIWQF-TNIWNDFLFGVAFSGADSKPITVGLNN 242

Query: 252 YLYPQNYL--WGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296
                + +  +    AAAV++GLP   V++   ++ V GLTAG VKG
Sbjct: 243 MANTSSSVKSYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 289


Lambda     K      H
   0.327    0.139    0.433 

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: 261
Number of extensions: 19
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: 296
Length of database: 289
Length adjustment: 26
Effective length of query: 270
Effective length of database: 263
Effective search space:    71010
Effective search space used:    71010
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: 48 (23.1 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