GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pantoea rwandensis LMG 26275

Align S-adenosylmethionine permease SAM3 (characterized)
to candidate WP_084936204.1 HA51_RS19300 L-asparagine permease

Query= CharProtDB::CH_091257
         (587 letters)



>NCBI__GCF_002095475.1:WP_084936204.1
          Length = 496

 Score =  188 bits (478), Expect = 4e-52
 Identities = 118/406 (29%), Positives = 203/406 (50%), Gaps = 16/406 (3%)

Query: 73  YQKVLSQRHLTMIAIGGTLGTGLFIGLGYSLASGPAALLIGFLLVGTSMFCVVQSAAELS 132
           YQK +  R + MIAIGG +GTGLF+G G  L     AL + +L+ G   F ++++  EL 
Sbjct: 26  YQKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLVCGIFSFFILRALGELV 85

Query: 133 CQFPVSGSYATHVSRFIDESVGFTVATNYALAWLISFPSELIGCALTISYWNQTVNPAVW 192
              P SGS+ ++   F+ E   +     Y + W ++   ++   AL + YW    +   W
Sbjct: 86  LHRPSSGSFVSYAREFLGEKASYVAGWMYFVNWAMTGIVDITAVALYMHYWGAFGDVPQW 145

Query: 193 VAIFYVFIMV--LNLFGVRGFAETEFALSIIKVIAIFIFIIIGIVLIAGGGPNSTGYIGA 250
           V       +V  +N+ GV+ FAE EF  ++IKV+AI +F+I+G+V +  G P      G 
Sbjct: 146 VFALGALAIVGTMNMIGVKWFAEMEFWFALIKVLAIAVFLIVGVVFLGSGKPLDGNTTGF 205

Query: 251 KYWHDPGAFAKPVFKNLCNTFVSAAFSFGGSELVLLTSTESKN-ISAISRAAKGTFWRIA 309
               D G                  F+F   ELV   + E K+  + + +A     WRI 
Sbjct: 206 HLITDNGGLFPHGLLPALVLVQGVVFAFASIELVGTAAGECKDPKTMLPKAINSVIWRIG 265

Query: 310 IFYITTVVIIGCLVPYNDPRLLSGSNSEDVSASPFVIALSNTGSMGAKVSNFMNVVILVA 369
           +FY+ +VV++  L+P+         N+     SPFV   S  G     + + MN+V+L A
Sbjct: 266 LFYVGSVVLLVLLLPW---------NAYQAGQSPFVTFFSKLGV--PYIGSVMNIVVLSA 314

Query: 370 VVSVCNSCVYASSRLIQALGASGQLPSVCSYMDRKGRPLVGIGISGAFGLLGFLVASKKE 429
            +S  NS +Y++ R+++++   G  P   S M ++  P  GI ++ A  ++G ++     
Sbjct: 315 ALSSLNSGLYSTGRILRSMSMGGSAPQFMSKMSKQQVPYAGILVTIAVYVVGVVLNYYVP 374

Query: 430 DEVFTWLFALCSISSFFTWFCICMSQIRFRMALKAQGRSNDEIAYK 475
            +VF  +  + S+    +W  I + Q+R R A+K +G++ D++++K
Sbjct: 375 SQVFEIVLNVASLGIISSWAFIVVCQMRLRKAIK-EGKA-DDVSFK 418


Lambda     K      H
   0.324    0.138    0.417 

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: 586
Number of extensions: 29
Number of successful extensions: 4
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: 587
Length of database: 496
Length adjustment: 35
Effective length of query: 552
Effective length of database: 461
Effective search space:   254472
Effective search space used:   254472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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