GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Pseudomonas fluorescens FW300-N1B4

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate Pf1N1B4_1144 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::Q9HY57
         (585 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1144
          Length = 579

 Score =  812 bits (2097), Expect = 0.0
 Identities = 429/574 (74%), Positives = 478/574 (83%), Gaps = 1/574 (0%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           MKLAIVTACP G VTSVL ARLL  AA+R GW T VE    + PE +LSA  I  A+WVL
Sbjct: 1   MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVL 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120
           LV   P+  +RFVGK V+++ PA+AL D  A L+R    A V VA + A   A    +AP
Sbjct: 61  LVTSAPVDMSRFVGKRVFQSTPAQALQDVEAVLRRGVEEAEVYVAPEVAAEPAAAVKSAP 120

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           R+VAVTACPTGVAHTFMAAEALQ AA +LG+ LQVETQGSVGARNPL    IA ADVVLL
Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAEAIADADVVLL 180

Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGVY 240
           AADI+V T RFAGKKIYRCGTG+ALKQA ATL +ALAEG+ ESA   +   A+ EK G+Y
Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLNKALAEGKQESASTGAKGPAKQEKTGIY 240

Query: 241 KHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPMLAG 299
           KHLLTGVSFMLPMVVAGGL+IALS  FGI A+K+ G+LAA L  +G DTAF LMVP+LAG
Sbjct: 241 KHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEEGTLAAALMQIGGDTAFKLMVPLLAG 300

Query: 300 YIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALK 359
           YIAYSIADRPGLAPGM+GGLLA TLGAGFIGGI+AGFIAGYAA+AI+   RLP SLEALK
Sbjct: 301 YIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFIAGYAAQAINRYARLPQSLEALK 360

Query: 360 PILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLG 419
           PIL+IPLLASL TGL+M+YVVGKPVAGMLA LT FLD MGT+NAILLG+LLGGMMCVDLG
Sbjct: 361 PILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTHFLDSMGTTNAILLGVLLGGMMCVDLG 420

Query: 420 GPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAAS 479
           GP+NKAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT +ARRKFA++ER+AGKAA 
Sbjct: 421 GPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAAL 480

Query: 480 VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNAI 539
           VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFVML+PNAI
Sbjct: 481 VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVMLIPNAI 540

Query: 540 NHALAYLLAIVAGSLLTGLLYAVLKRGAEPGLAL 573
           NHAL YLLAIVAGSLLT + YA+LKR     LAL
Sbjct: 541 NHALLYLLAIVAGSLLTAVTYALLKRPETVELAL 574


Lambda     K      H
   0.321    0.137    0.392 

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: 973
Number of extensions: 39
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: 585
Length of database: 579
Length adjustment: 36
Effective length of query: 549
Effective length of database: 543
Effective search space:   298107
Effective search space used:   298107
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 (21.9 bits)
S2: 53 (25.0 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