GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1749 in Pseudomonas fluorescens GW456-L13

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate PfGW456L13_3346 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)

Query= TCDB::Q9X271
         (324 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3346 Oligopeptide
           transport system permease protein OppB (TC 3.A.1.5.1)
          Length = 536

 Score =  229 bits (583), Expect = 2e-64
 Identities = 122/253 (48%), Positives = 173/253 (68%), Gaps = 1/253 (0%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN-G 62
           L+ V +L V F       +AV+G+S+ + +GE+L +VGESGSGKSV+  S+LRL+     
Sbjct: 6   LIEVRDLSVNFVVGNRCQRAVEGVSFDIKRGETLALVGESGSGKSVTAHSILRLLPYPLA 65

Query: 63  RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122
           R   G  ++ G++LL+L ++ +R+IRG  I++IFQ PMTSLNP+  +  Q+ E +  H+ 
Sbjct: 66  RHPSGTILYSGQNLLELKEKTIRHIRGNRIAMIFQEPMTSLNPLHSIEKQINEVLGIHKG 125

Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182
           +  + A +R +ELLE VGIPE  KR    P + SGG RQRVMIAMALA  P+LLIADEPT
Sbjct: 126 LTGKVATKRTLELLEMVGIPEPHKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPT 185

Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242
           TALDVT+Q +I+ELL+EL+   GM+++ I+HDL++      R+  M  G IVE+A  EE+
Sbjct: 186 TALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQQGCIVEQASCEEL 245

Query: 243 LKTPLHPYTKGLL 255
            + P HPYT+ LL
Sbjct: 246 FRAPQHPYTRELL 258



 Score =  180 bits (456), Expect = 8e-50
 Identities = 107/262 (40%), Positives = 164/262 (62%), Gaps = 17/262 (6%)

Query: 4   LLNVNNLKVEFHRVEGI-------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56
           LL V +LKV F   +G+       VKAVDGI++ L +G++LGIVGESGSGKS   L++LR
Sbjct: 275 LLAVEDLKVWFPIKKGLLKRTVDYVKAVDGINFSLPQGQTLGIVGESGSGKSTLGLAILR 334

Query: 57  LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116
           LI   G I      F G+ L  L ++++R +R +++ ++FQ+P  SL+P + V   V E 
Sbjct: 335 LIASKGAIR-----FEGQQLDCLTQQQVRPLR-REMQVVFQDPFGSLSPRMCVSQIVGEG 388

Query: 117 IIWHRLMKNEEARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKL 175
           +  H++    E  +  I  L+ VG+ PE+  R   YP +FSGG RQR+ IA AL   P L
Sbjct: 389 LRIHKMGTEAEQEQAIIAALKEVGLDPETRHR---YPHEFSGGQRQRIAIARALVLKPAL 445

Query: 176 LIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVE 235
           ++ DEPT+ALD T+Q Q++ELL+ L+ +Y ++ +FI+HDL+V      +++ +  G++VE
Sbjct: 446 ILLDEPTSALDRTVQRQVVELLRSLQTKYNLTYLFISHDLAVVKALSHQLMVVKHGQVVE 505

Query: 236 EAPVEEILKTPLHPYTKGLLNS 257
           +   + I   P HPYT+ LL +
Sbjct: 506 QGDAQSIFAAPQHPYTQQLLEA 527


Lambda     K      H
   0.320    0.139    0.401 

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: 445
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: 324
Length of database: 536
Length adjustment: 31
Effective length of query: 293
Effective length of database: 505
Effective search space:   147965
Effective search space used:   147965
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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