GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_17540
          Length = 837

 Score =  640 bits (1650), Expect = 0.0
 Identities = 370/831 (44%), Positives = 509/831 (61%), Gaps = 17/831 (2%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APLSG +L L  VPD VF+S  +GDG+ IDP + TL AP    + ++  +GHAV++
Sbjct: 8   LILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVARTGHAVTL 67

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             DNG ++L+H+GLDTV L G+GF+ LV+EG RV  GQPL+ +D D VAL  +SL++L++
Sbjct: 68  RADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCKSLVSLLV 127

Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPS--GAVEAVDEEEGDALFSKPLTLPNANGLHA 182
           + +GE F      L  V+ G+PLL +     G  E  D++ G  +F + + + +  GLHA
Sbjct: 128 ITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQ-VRIAHRGGLHA 186

Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242
           RPAA+  Q A+GF +   LH   +SA+  S++ +M L   +   + VS  G DAEAA++A
Sbjct: 187 RPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDAEAALQA 246

Query: 243 LVALLAEGCGE---AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQG 299
           L+  L+    E   A     EP    +   +L GVCA+PG   G +V+++  +L     G
Sbjct: 247 LLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQLPEDIGG 306

Query: 300 TGGATERAALTRGLLAANEALQVLQDKAAGSAQAE---IFRAHQELLEDPTLLEHAHRLL 356
                +R  L+  L      + +  + A      +   IF AH  LLEDP LL+ A   +
Sbjct: 307 HAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAADLFI 366

Query: 357 GEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAW--DLP 414
            +G +A  AW+ +      + Q LG+ L+AERA DL D+ QRVL+++LG    AW  D+ 
Sbjct: 367 EQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLG---EAWQFDVA 423

Query: 415 ERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALA 474
             AI+ A++LTPS    L  + V G   V GGATSHVAILAR  GLP +  +  ++LA  
Sbjct: 424 AGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQE 483

Query: 475 NGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTA 534
            G+ V+LDAD G L L P +  + Q+  A+  +     +  + A  PA T DG  VEV A
Sbjct: 484 QGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAA 543

Query: 535 NVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVR 594
           NVAS  E   +L  G +GVGLLR+EFL++DR+ AP  EEQ   Y A+  A+G ++ +++R
Sbjct: 544 NVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMG-DKPVIIR 602

Query: 595 TLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPM 654
           T+DVGGDK L Y+P+ +E NP LGLRGIRL   RP LL +Q RA+L +    R  I+LPM
Sbjct: 603 TIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPM 662

Query: 655 VSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLT 714
           V+ + EL   RK L+     LGL+E P+LG+M+EVP+AAL+A+  A H DF SIGTNDL+
Sbjct: 663 VTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLS 722

Query: 715 QYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIG 774
           QYTLAMDRDH  LA + D+ HPA+LRLIA T   A  HG+WVGVCGALAS+ LA PVLIG
Sbjct: 723 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIG 782

Query: 775 LGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           LGV ELSVS P I  IK  VR LD A C  ++ ++L L  A  VR A  ++
Sbjct: 783 LGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRH 833


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: 1571
Number of extensions: 73
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: 837
Length adjustment: 42
Effective length of query: 796
Effective length of database: 795
Effective search space:   632820
Effective search space used:   632820
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