GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1A in Mesorhizobium ciceri WSM1271

Align major cell-binding factor (characterized)
to candidate YP_004143481.1 Mesci_4321 family 3 extracellular solute-binding protein

Query= CharProtDB::CH_021449
         (259 letters)



>NCBI__GCF_000185905.1:YP_004143481.1
          Length = 260

 Score = 93.6 bits (231), Expect = 4e-24
 Identities = 78/258 (30%), Positives = 124/258 (48%), Gaps = 21/258 (8%)

Query: 10  LAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEVDVA 69
           +AV AL     F+  +A    LE IK+ G+L + +    P +  ++    E+ GF+ D+ 
Sbjct: 8   IAVAALLLASTFTAVSARADDLEKIKAAGELKISMSGQYPPFNFVNDQN-EVVGFDADIG 66

Query: 70  KLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDA 129
           K +A+ I G    I   A +    G LL N   D V+ + TITPER+++ +F  PYY   
Sbjct: 67  KAIAERI-GVKGTIITTAWDGIIAG-LLTN-KYDTVVGSMTITPEREKVVDFVGPYYHAG 123

Query: 130 IGLLVLKEKKYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAAL 189
             + V ++ K +SL D+KG  IGV    T +K    A +K G D++   +   P +   L
Sbjct: 124 RAVFVSEQSKVQSLDDLKGKTIGVTLGETHEK---WAREKGGWDIR--TYKGLPELLLEL 178

Query: 190 DAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQ------SYGIVTKKDDP----AFAKYV 239
            A RVDA  VD   ++  V +  E +     P       + GI  +KD+P    A  K +
Sbjct: 179 RAGRVDAIVVDNIPVMVAVKETGEKVRKLNTPDIEGGAVAIGIAIRKDNPELKAAMQKAL 238

Query: 240 DDFVKEHKNEIDALAKKW 257
           DD + +     + ++ KW
Sbjct: 239 DDMLAD--GSYEKISMKW 254


Lambda     K      H
   0.316    0.135    0.372 

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: 156
Number of extensions: 6
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: 259
Length of database: 260
Length adjustment: 24
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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 (21.6 bits)
S2: 47 (22.7 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