GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisJ in Pseudomonas fluorescens FW300-N2C3

Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate AO356_23515 AO356_23515 ABC transporter substrate-binding protein

Query= CharProtDB::CH_014295
         (260 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23515
          Length = 256

 Score =  254 bits (649), Expect = 1e-72
 Identities = 124/257 (48%), Positives = 169/257 (65%), Gaps = 4/257 (1%)

Query: 1   MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELC 60
           MKK ++ L LV   +S   ++ A  + +R G DPTY PFESK   G L GFDI+L + LC
Sbjct: 1   MKKYLIGLMLV---ASPLMSWGA-NEELRFGVDPTYPPFESKRPDGSLTGFDIELGESLC 56

Query: 61  KRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK 120
             +  +C +VEN  D ++ +LK +K D I+S+LSITE R+ EIAF++ LY   +RLV  +
Sbjct: 57  SELQRRCVWVENAFDGMVSALKGRKFDGILSALSITEARKAEIAFSNTLYDTPARLVAPE 116

Query: 121 NSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAA 180
            S +QPT ESL+GKR+GV QG+  E +    W  KG+E+V YQ  D  YSDL  GR+DAA
Sbjct: 117 GSPLQPTAESLRGKRIGVQQGSVFEVYAKRMWGLKGVEVVPYQSSDLTYSDLINGRLDAA 176

Query: 181 FQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240
           F D +A SEG LK+P GK + + G  VK  ++FG GTG+GLRK D  L   +N+A   + 
Sbjct: 177 FDDAIAVSEGLLKKPAGKGFGYAGEVVKSPEIFGPGTGIGLRKSDTALAGEINQALERLH 236

Query: 241 ADGTYEKLAKKYFDFDV 257
            +GTYE++A KYFDFD+
Sbjct: 237 RNGTYERIASKYFDFDI 253


Lambda     K      H
   0.315    0.133    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: 213
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
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 17 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