GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Pseudomonas simiae WCS417

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF2386 PS417_12165 microcin ABC transporter ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__WCS417:GFF2386
          Length = 523

 Score =  228 bits (580), Expect = 3e-64
 Identities = 121/251 (48%), Positives = 174/251 (69%), Gaps = 7/251 (2%)

Query: 13  LLQTVDLKKYFPQG------KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66
           +LQ  DL   F  G      K  L+AVDGIS+ ++ G+TLG+VGESG GKSTLG+ IL+L
Sbjct: 267 VLQVDDLTVQFRLGGGLFRRKTYLRAVDGISLSVQRGKTLGIVGESGSGKSTLGQAILRL 326

Query: 67  LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
           L    G I F+G+ +  LN+++M+P+RK+MQ++FQDP GSL+P+MTV +II + L +H  
Sbjct: 327 L-DSTGSIRFQGEALDPLNNQQMRPWRKQMQVVFQDPYGSLSPRMTVEQIISEGLEVHAP 385

Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186
            +  +R  +V ++L  VG+     + +PHEFSGGQ+QRI IARAL L P  ++ DEP SA
Sbjct: 386 CSLADRDAQVIQVLKDVGLDPASRHRYPHEFSGGQRQRIAIARALVLKPALMLLDEPTSA 445

Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246
           LD ++Q Q++ LL E+Q K G++YLFI+H+LAVV  ++H + V+  G++VE G    +F 
Sbjct: 446 LDRTVQKQVVALLRELQDKYGLTYLFISHDLAVVRAMAHDMIVIKDGQVVERGASHAVFD 505

Query: 247 NPIHPYTRALL 257
            P HPYT+ LL
Sbjct: 506 APQHPYTKELL 516



 Score =  178 bits (451), Expect = 3e-49
 Identities = 96/236 (40%), Positives = 154/236 (65%), Gaps = 7/236 (2%)

Query: 33  VDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG----GKIFFEGKDITNLNDKE 88
           V  +S++++ GE L LVGESG GKS    +IL+LL   G    G I + G+++   +   
Sbjct: 19  VRNLSLDVRPGECLALVGESGSGKSVTAHSILQLLPEAGTETTGSIQYRGQELIGASAAT 78

Query: 89  MKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGR 147
           ++  R  ++ +IFQ+P+ SLNP  ++ + I + L++HK    K  + R+ ELLD+VGI +
Sbjct: 79  LQKLRGNRIAMIFQEPMTSLNPLHSIEKQIGETLLLHKGLGGKAAQARILELLDLVGIQK 138

Query: 148 --EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQK 205
             E + ++PH+ SGGQ+QR+ IA ALA  P+ ++ DEP +ALDV++Q +I+ LL+ +Q++
Sbjct: 139 PQERLKAYPHQLSGGQRQRVMIAMALACEPELLIADEPTTALDVTVQRKILLLLKSLQKR 198

Query: 206 MGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVP 261
           +G+S L I+H+L +V  I+ +V VM  G+IVE  D   +F  P HPY+R LL + P
Sbjct: 199 LGMSLLLISHDLNLVRSIAQRVCVMRAGEIVEQADCQTLFNAPQHPYSRLLLDAEP 254


Lambda     K      H
   0.321    0.142    0.417 

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: 502
Number of extensions: 20
Number of successful extensions: 5
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: 328
Length of database: 523
Length adjustment: 31
Effective length of query: 297
Effective length of database: 492
Effective search space:   146124
Effective search space used:   146124
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: 50 (23.9 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