Alignments for a candidate for mglA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudomonas simiae WCS417

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate GFF2144 PS417_10935 xylose transporter

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__WCS417:GFF2144
          Length = 518

 Score =  400 bits (1028), Expect = e-116
 Identities = 221/499 (44%), Positives = 326/499 (65%), Gaps = 12/499 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD--EGEI 61
           +L++  I K F GV+AL G+ +   PGE   + GENGAGKSTLMK+++ VY     EGEI
Sbjct: 8   LLQMNGIVKSFGGVNALNGIDIRVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWEGEI 67

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMYRE 120
           +++G+ ++    SE   AGIV + QEL+++ +LSVAENIFMG E    G  ++Y  M+  
Sbjct: 68  LWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMFHR 127

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           AE  M+E    +++    + +Y    QQ+VEIA+A+ K+A++LILDEP+S+LT+ E E L
Sbjct: 128 AEALMRELKVPDMNVALPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 187

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
            ++++ LK KGVA ++ISH+L+E+  +CD ++V+RDG++I T ++ ++   KI+  MVGR
Sbjct: 188 LDIIRGLKAKGVACVYISHKLDEVAAVCDTIAVIRDGKHIATTAMADMDIAKIITQMVGR 247

Query: 241 KLEKFYIKEAHEPGEVVLEVKNLS--------GERFENVSFSLRRGEILGFAGLVGAGRT 292
           ++   Y  E H  GEV+ E +N++         +R ++VSF L+RGEILG AGLVGAGRT
Sbjct: 248 EMSNLYPTEPHAVGEVIFEARNVTCHDVDNPKRKRVDDVSFVLKRGEILGIAGLVGAGRT 307

Query: 293 ELMETIFGFRPKR-GGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV 351
           EL+  +FG  P R   E++++G+ ++   PL +I  G+ +VPEDRK+ G+I  + +  N+
Sbjct: 308 ELVSALFGAYPGRYSAEVWLDGQVIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQNI 367

Query: 352 SLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411
           +L  LD       I  + E    D  I    ++ A     +  LSGGNQQK VLAK L  
Sbjct: 368 TLTVLDSYAHRTRIDAEAELGSIDQQIARMHLKTASTFLPITSLSGGNQQKAVLAKMLMA 427

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           KPK+LILDEPTRG+DVGAK EIY++M  LA EGV +IM+SSEL EVL +SDR+ V+  G+
Sbjct: 428 KPKVLILDEPTRGVDVGAKYEIYKLMGALAAEGVAIIMVSSELAEVLGVSDRVLVIGDGQ 487

Query: 472 LAGIIDAKEASQEKVMKLA 490
           L G    +  +QE+V+  A
Sbjct: 488 LRGDFINEGLTQEQVLAAA 506



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 65/242 (26%), Positives = 110/242 (45%), Gaps = 15/242 (6%)

Query: 260 VKNLSGERFEN-VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRG--GEIYIEGKRV 316
           VK+  G    N +   +R GE +G  G  GAG++ LM+ +    P     GEI  +G+ +
Sbjct: 15  VKSFGGVNALNGIDIRVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWEGEILWDGQPL 74

Query: 317 EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKG----PFISFKREKE 372
           +     +    GI ++ ++   L L+  +S+  N+ +     +  G    P +  + E  
Sbjct: 75  KAQSISETEAAGIVIIHQE---LTLVPDLSVAENIFMGHELTLPGGRMNYPAMFHRAEAL 131

Query: 373 LADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAE 432
           + +  +K  D+  A P   V    GG QQ V +AK L  + ++LILDEP+  +       
Sbjct: 132 MRE--LKVPDMNVALP---VSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEV 186

Query: 433 IYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           +  I+  L  +GV  + IS +L EV  + D IAV+  GK        +    K++    G
Sbjct: 187 LLDIIRGLKAKGVACVYISHKLDEVAAVCDTIAVIRDGKHIATTAMADMDIAKIITQMVG 246

Query: 493 LE 494
            E
Sbjct: 247 RE 248


Lambda     K      H
   0.318    0.138    0.385 

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: 674
Number of extensions: 34
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 494
Length of database: 518
Length adjustment: 34
Effective length of query: 460
Effective length of database: 484
Effective search space:   222640
Effective search space used:   222640
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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