GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Shewanella sp. ANA-3

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 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__ANA3:7024900
          Length = 499

 Score =  387 bits (993), Expect = e-112
 Identities = 204/499 (40%), Positives = 324/499 (64%), Gaps = 10/499 (2%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M  ILE+K I K +PGV AL+ VS+  + GEVHA++GENGAGKSTL+K++ G    D G+
Sbjct: 1   MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           I++ G    +N P +A  AGI TV+QE++++ NL+VA+N+F+G E +R   I +KKMY +
Sbjct: 61  ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A   + + F ++ID    L  YSIA+QQ++ IAR V   AKVL+LDEPT+SL  KE + L
Sbjct: 121 ARAVLTQ-FKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F ++  LK KGVAI+FI+H L+++++I D+++VLR+G++IG      L + K++E M+GR
Sbjct: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239

Query: 241 KLEKFYIKEAHEPGEVV--------LEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRT 292
            L++  + +  +   V         LE  ++ G   ++++ ++ +G+ +G AGL+G+GR+
Sbjct: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS-IQSMNLTVPKGQAVGLAGLLGSGRS 298

Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
           E+   +FG      G I++ G+++ ++ P+DAI  GI L PEDRK  G+I  +SI  N+ 
Sbjct: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358

Query: 353 LPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412
           L    RI    ++S  R++E+A + I    I     D+ +  LSGGNQQKV+LA+WLA++
Sbjct: 359 LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418

Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472
           P +L+LDEPTRGID+GA AEI +++  L  EG+ +++ SSEL E++  S+++ V+     
Sbjct: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478

Query: 473 AGIIDAKEASQEKVMKLAA 491
              +   E + + VM+  A
Sbjct: 479 VRELSGAELTSQHVMQAIA 497



 Score = 92.8 bits (229), Expect = 2e-23
 Identities = 70/246 (28%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 256 VVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310
           ++LE+K +S      +  E+VS  L  GE+    G  GAG++ L++ + G + K  G+I 
Sbjct: 3   LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62

Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKRE 370
             G+    N P+DA + GI  V ++   + L+  +++  N+ L    R  +   I FK+ 
Sbjct: 63  FLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPR--RLGLIHFKKM 117

Query: 371 KELADWAIKTF----DIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGID 426
              A   +  F    D+     D  +       QQ + +A+ +A+  K+L+LDEPT  +D
Sbjct: 118 YADARAVLTQFKLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLD 172

Query: 427 VGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKV 486
                 ++ I++QL  +GV ++ I+  L +V Q+SDRI V+  G+  G     E  Q K+
Sbjct: 173 AKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKL 232

Query: 487 MKLAAG 492
           ++   G
Sbjct: 233 IEAMLG 238


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: 596
Number of extensions: 28
Number of successful extensions: 7
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: 499
Length adjustment: 34
Effective length of query: 460
Effective length of database: 465
Effective search space:   213900
Effective search space used:   213900
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 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