GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Pseudomonas putida KT2440

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Putida:PP_3817
          Length = 382

 Score =  217 bits (553), Expect = 4e-61
 Identities = 138/375 (36%), Positives = 202/375 (53%), Gaps = 27/375 (7%)

Query: 2   TSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIF 61
           T VS+R L+ ++G  T +D L+L+I  GEFL  LGSSG GKST L+ +AG    S G+I 
Sbjct: 13  TLVSLRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEIL 72

Query: 62  IKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEIL 121
           +  +++    P  R IGMVFQ Y+L+P + V  N++F L + K+  AE  KRV    +++
Sbjct: 73  VDGQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLV 132

Query: 122 QIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQ 181
           Q++    RKPS++SGGQ+QRVAI RALV +  + L DEPL  LD KLR +L+ E+++LH+
Sbjct: 133 QLEQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHR 192

Query: 182 SLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNF 241
            L  T++YVTHDQ EA+ L+ RIA+   G I  L     +Y  P N FVA F+G  + NF
Sbjct: 193 RLGITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLG--NSNF 250

Query: 242 FRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPG----QKVVLGLRPEHVKVDEARDG- 296
            R +       SF             P   RL PG    Q  ++ +RPE      A    
Sbjct: 251 LRIKASSNGAGSF----------EGQPVAIRLTPGLAASQDALIMVRPEKAVAMSAEQAM 300

Query: 297 -EPTHQAVVDIEEPMGADNLLW-------LTFAGQSMSVRIAGQRRYP--PGSTVRLSFD 346
            EP      ++   +G    L        +T  G  ++V+       P  PG +V++ + 
Sbjct: 301 REPLPAGWNEVTAKVGEVLFLGESQTCHVVTAGGTELTVKALSAAGMPMQPGDSVKVRWA 360

Query: 347 MGVASIFDAESENRL 361
           +  A I+   +E+ L
Sbjct: 361 VADACIYTEWAESDL 375


Lambda     K      H
   0.320    0.137    0.392 

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: 333
Number of extensions: 11
Number of successful extensions: 1
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: 361
Length of database: 382
Length adjustment: 30
Effective length of query: 331
Effective length of database: 352
Effective search space:   116512
Effective search space used:   116512
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: 49 (23.5 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