GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS03640 in Pseudomonas fluorescens FW300-N2E2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG

Query= uniprot:D8IZC7
         (521 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 D-xylose transport
           ATP-binding protein XylG
          Length = 518

 Score =  375 bits (962), Expect = e-108
 Identities = 213/506 (42%), Positives = 318/506 (62%), Gaps = 21/506 (4%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPD--QGEI 63
           LLQM GI K+FG   AL+ + + +RPGE   L GENGAGKSTLMKVLS V+      GEI
Sbjct: 5   LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEI 64

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
           L DG+P+  +    + AAGI +I+QEL + P++SVA N+FMG EL    G +++ AM  R
Sbjct: 65  LWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIHR 124

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAE-----QQQVEIARALVHRSRIVIMDEPTAALSERE 178
            +A++R+L       D+   L +++     QQ VEIA+AL  ++R++I+DEP++AL+  E
Sbjct: 125 AEALMRELKV----PDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSE 180

Query: 179 TEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQM 238
            E L +++R L+ +G+A +YISH++ EV A+ D ++V+RDG  +      ++   +I+  
Sbjct: 181 IEVLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQ 240

Query: 239 MVGRSLSEFYQHQRIAPADAAQLP------TVMQVRALAGGKIRPASFDVRAGEVLGFAG 292
           MVGR +S  Y  +   P D  ++       T   V      ++   SF ++ GE+LG AG
Sbjct: 241 MVGREMSNLYPTE---PHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAG 297

Query: 293 LVGAGRTELARLLFGADP-RSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQ 351
           LVGAGRTEL   LFGA P R  G++ L G+ +    P  ++RAG+  VPEDRK QG+   
Sbjct: 298 LVGAGRTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPD 357

Query: 352 MAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVL 411
           + V  N T+ V   +++L  + + +  G     I R+++K A P  P+  LSGGNQQK +
Sbjct: 358 LGVGQNITLAVLDNYSKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAV 417

Query: 412 LARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRV 471
           LA+ L   P+VLILDEPTRGVD+ AK EIY+L+  LA++GV+++++SSEL EV+G+ DRV
Sbjct: 418 LAKMLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRV 477

Query: 472 LVMREGMITGELAGAAITQENIMRLA 497
           LV+ +G + G+     +TQE ++  A
Sbjct: 478 LVIGDGQLRGDFINHELTQEQVLAAA 503


Lambda     K      H
   0.320    0.135    0.378 

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: 659
Number of extensions: 27
Number of successful extensions: 9
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: 518
Length adjustment: 35
Effective length of query: 486
Effective length of database: 483
Effective search space:   234738
Effective search space used:   234738
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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