GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlE in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-mannitol and D-mannose, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_4850 Various polyols ABC transporter, periplasmic substrate-binding protein

Query= reanno::pseudo3_N2E3:AO353_25880
         (436 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4850 Various polyols ABC
           transporter, periplasmic substrate-binding protein
          Length = 440

 Score =  830 bits (2144), Expect = 0.0
 Identities = 407/436 (93%), Positives = 419/436 (96%)

Query: 1   MKPTVKALLACTCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60
           M+P+VKALLA TCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL
Sbjct: 1   MQPSVKALLALTCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60

Query: 61  EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPAGYALDDVFPSVRE 120
           EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPA YALDDVFPSVRE
Sbjct: 61  EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYALDDVFPSVRE 120

Query: 121 GLSVKGTLYALPFYAESSMTYYRTDLFKDAGLAMPEHPTWEQIGEFAGKLNKPDQEQYGI 180
           GLSVKGTLYALPFYAESS+TYYRTDLFKDAGL MPE PTW QI EFA KL   D+EQYGI
Sbjct: 121 GLSVKGTLYALPFYAESSITYYRTDLFKDAGLTMPERPTWTQISEFASKLTNKDKEQYGI 180

Query: 181 CLRGKAGWGENMALITTIANAYGARWFDEKWQPEFSGPEWKNALSFYADTMKKSGPPGAS 240
           CLRGKAGWGENMALITT+ANAYGARWFDE+W+PEF GPEWKNAL+FY DTMKKSGPPGAS
Sbjct: 181 CLRGKAGWGENMALITTVANAYGARWFDEQWKPEFIGPEWKNALNFYVDTMKKSGPPGAS 240

Query: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVSEHVGFTYAPHQVTDKGSAWLYS 300
           SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVS+HVGFTYAPH+ TDKGSAWLYS
Sbjct: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVSDHVGFTYAPHETTDKGSAWLYS 300

Query: 301 WALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYSEAYMNAAPFA 360
           WALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTY+EAYMNAAPFA
Sbjct: 301 WALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYTEAYMNAAPFA 360

Query: 361 KVTLESLKVADPGKPTLKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQALAA 420
           KVTLESLK ADP KP+LKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQAL A
Sbjct: 361 KVTLESLKAADPSKPSLKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQALTA 420

Query: 421 AQQTTEREMKRAGYPK 436
           AQ TTEREMKRAGYPK
Sbjct: 421 AQSTTEREMKRAGYPK 436


Lambda     K      H
   0.315    0.130    0.391 

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: 819
Number of extensions: 10
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: 436
Length of database: 440
Length adjustment: 32
Effective length of query: 404
Effective length of database: 408
Effective search space:   164832
Effective search space used:   164832
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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