GapMind for catabolism of small carbon sources

 

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

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_04460 AO353_04460 PTS N-acetyl-D-glucosamine transporter

Query= reanno::WCS417:GFF4500
         (838 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04460
          Length = 838

 Score =  661 bits (1706), Expect = 0.0
 Identities = 385/831 (46%), Positives = 522/831 (62%), Gaps = 16/831 (1%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APLSG +L L KVPDPVF+S  +GDG+ IDP + TL AP AGV+ ++  +GHAV++
Sbjct: 8   LTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVARTGHAVTL 67

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             DNG ++L+H+GLDTV L G+GF+ LV+EG RV  GQ L+ FD D VA   +SL++L++
Sbjct: 68  RADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCKSLVSLLV 127

Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPSGAVEA-VDEEEGDALFSKPLTLPNANGLHAR 183
           + + E F +L   L  V+ G+PLL + P     A V+ +   A     + + +  GLHAR
Sbjct: 128 LTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIHRGGLHAR 187

Query: 184 PAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKAL 243
           PAA+  Q A  FN+   LH   +SA+  SL+ +M L   + D +QVS  G DA+AA++AL
Sbjct: 188 PAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKAALQAL 247

Query: 244 VALLAEGCGE-----AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQ 298
           +  L+    +     A   +A+   T + A +L GVCA+PG   G + Q+    L   + 
Sbjct: 248 LNALSTAVNDDSHAAAPTPIAQRTRT-AEAGVLNGVCAAPGLVGGPLFQLAAIPLP-EDT 305

Query: 299 GTGGATERA-ALTRGL-LAANEALQVLQD--KAAGSAQAEIFRAHQELLEDPTLLEHAHR 354
           G   A E+  AL R L    +E  + L    K   + + +IF AH  LLEDP LLE A +
Sbjct: 306 GKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQ 365

Query: 355 LLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLP 414
            + +G +A  AW+ +  A   + Q LGN L+AERA DL D+ QRVL+ +LG QD  +D+P
Sbjct: 366 SIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLG-QDWHYDVP 424

Query: 415 ERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALA 474
             AI+ A +LTPS    L  + V G     GGATSHVAILAR  GLP +  + A +L   
Sbjct: 425 AGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQP 484

Query: 475 NGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTA 534
            G+ V+LDAD G L L P+   +EQ+  A++  + R +R  AQA  PA TRDG  +EV A
Sbjct: 485 QGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAA 544

Query: 535 NVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVR 594
           NVAS  E   AL  G +GVGLLR+EFL++DR  AP  +EQ   Y A+  A+G ++++++R
Sbjct: 545 NVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMG-DKSVIIR 603

Query: 595 TLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPM 654
           T+DVGGDK L Y+P+ AE NP LGLRGIR+   RP+LL +Q RA+L  +   R  I+LPM
Sbjct: 604 TIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPM 663

Query: 655 VSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLT 714
           V+ + EL   R+ L+     L LT+  +LG+MIEVP+AAL+A+  A H DF SIGTNDL+
Sbjct: 664 VTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTNDLS 723

Query: 715 QYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIG 774
           QYTLAMDRDH  LA + D+ HPA+LRLIA T   A  H +WVGVCGALAS+ LA PVLIG
Sbjct: 724 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPVLIG 783

Query: 775 LGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           LG+ ELSVS P +  IK  VR+LD ADC+  +  +L L  A  VR A  Q+
Sbjct: 784 LGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQH 834


Lambda     K      H
   0.318    0.133    0.371 

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: 1530
Number of extensions: 68
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: 838
Length of database: 838
Length adjustment: 42
Effective length of query: 796
Effective length of database: 796
Effective search space:   633616
Effective search space used:   633616
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 (21.7 bits)
S2: 56 (26.2 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