Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_05485 AO353_05485 PTS fructose transporter subunit IIA

Query= reanno::pseudo3_N2E3:AO353_05485
         (953 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05485
          Length = 953

 Score = 1827 bits (4732), Expect = 0.0
 Identities = 953/953 (100%), Positives = 953/953 (100%)

Query: 1   MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAI 60
           MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAI
Sbjct: 1   MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAI 60

Query: 61  PHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET 120
           PHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET
Sbjct: 61  PHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET 120

Query: 121 DLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180
           DLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS
Sbjct: 121 DLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180

Query: 181 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE 240
           NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE
Sbjct: 181 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGE 240

Query: 241 AHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPA 300
           AHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPA
Sbjct: 241 AHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPA 300

Query: 301 KILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPA 360
           KILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPA
Sbjct: 301 KILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPA 360

Query: 361 LLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQV 420
           LLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQV
Sbjct: 361 LLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQV 420

Query: 421 LQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELT 480
           LQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELT
Sbjct: 421 LQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELT 480

Query: 481 DEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP 540
           DEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP
Sbjct: 481 DEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP 540

Query: 541 SEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600
           SEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV
Sbjct: 541 SEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600

Query: 601 LRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAV 660
           LRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAV
Sbjct: 601 LRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAV 660

Query: 661 EVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPL 720
           EVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPL
Sbjct: 661 EVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPL 720

Query: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM 780
           VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM
Sbjct: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM 780

Query: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840
           FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND
Sbjct: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840

Query: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900
           LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL
Sbjct: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900

Query: 901 VGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL 953
           VGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL
Sbjct: 901 VGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL 953


Lambda     K      H
   0.319    0.135    0.383 

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: 2482
Number of extensions: 68
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: 953
Length of database: 953
Length adjustment: 44
Effective length of query: 909
Effective length of database: 909
Effective search space:   826281
Effective search space used:   826281
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 (21.7 bits)
S2: 57 (26.6 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources