GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens FW300-N2E2

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  952 bits (2462), Expect = 0.0
 Identities = 486/518 (93%), Positives = 503/518 (97%), Gaps = 1/518 (0%)

Query: 1   MFASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMG 60
           MFASATASS P +  +P+ IP DEPYLLE++NVSKGFPGVVALSDVQLRVRPGSVLALMG
Sbjct: 1   MFASATASSAPAMTFRPDVIP-DEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMG 59

Query: 61  ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA 120
           ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA
Sbjct: 60  ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA 119

Query: 121 ENIWIGREQLNGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVS 180
           ENIWIGREQLNG HM+DH EMHRCTA+LLERLRI LDPEEQVGNLSIAERQMVEIAKAVS
Sbjct: 120 ENIWIGREQLNGLHMVDHGEMHRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVS 179

Query: 181 YDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDG 240
           YDSDILIMDEPTSAIT+ EVAHLFSIIADLK+QGKGIIYITHKMNEVF+IADEVAVFRDG
Sbjct: 180 YDSDILIMDEPTSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDG 239

Query: 241 AYIGLQRADSMDGDSLISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLH 300
           AYIGLQRADSMDGDSLISMMVGRELSQLFPVRE+PIGDL++SVRDL LDG+FKGVSFDLH
Sbjct: 240 AYIGLQRADSMDGDSLISMMVGRELSQLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLH 299

Query: 301 AGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDR 360
           AGEILGIAGLMGSGRTNVAEAIFG+TPS GGEI LDGQPVRISDPHMAIEKGFALLTEDR
Sbjct: 300 AGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDR 359

Query: 361 KLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS 420
           KLSGLFPCLSVLENMEMAVLPHY GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS
Sbjct: 360 KLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS 419

Query: 421 GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE 480
           GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE
Sbjct: 420 GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE 479

Query: 481 VLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 518
           VLGMSDRVMVMHEGDLMGTL+R EATQERVMQLASG+S
Sbjct: 480 VLGMSDRVMVMHEGDLMGTLNRGEATQERVMQLASGLS 517


Lambda     K      H
   0.321    0.137    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: 1012
Number of extensions: 21
Number of successful extensions: 6
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: 521
Length of database: 517
Length adjustment: 35
Effective length of query: 486
Effective length of database: 482
Effective search space:   234252
Effective search space used:   234252
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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 (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