GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05180
          Length = 386

 Score =  310 bits (793), Expect = 5e-89
 Identities = 174/368 (47%), Positives = 243/368 (66%), Gaps = 15/368 (4%)

Query: 1   MSELQLSDVRKSYG-GL-EVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSG 58
           M+ L+L +V K+YG GL + +K ++L IK GEF++ VGPSGCGKSTL+  IAGLE I+ G
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 59  DLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAA 118
            + I D  ++ + P  R IAMVFQSYALYP M+VREN+ F L+   + ++ I++ VN  A
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120

Query: 119 HILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIAR 178
            +L++  LL+RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA+LRV MR E+  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPK 238
           +H++L TT VYVTHDQ+EAMTL DK+ VM+ G+++Q G+P D+Y +PANLFVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240

Query: 239 MNFLKGVIEIDEDQAYARLPDYGDAK--IPVTLQAAA--GTAVTIGIRPEHFDEAGP--- 291
           MNF+   ++  + +  A L D G A+  +P+ +Q A      V +G+RPE    AG    
Sbjct: 241 MNFIPLRLQRKDGRLLALL-DSGQARCELPMGMQDAGLEDREVILGMRPEQIMLAGSEPN 299

Query: 292 --AALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVF 349
               +   + + E  G +T  +     N   +          + G+ LT +FDP  VL+F
Sbjct: 300 GLPTIRAEVQVTEPTGPDTLVFVSL--NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLF 357

Query: 350 DGE-GKRL 356
           D + G+RL
Sbjct: 358 DAQSGERL 365


Lambda     K      H
   0.321    0.139    0.396 

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: 391
Number of extensions: 14
Number of successful extensions: 2
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: 358
Length of database: 386
Length adjustment: 30
Effective length of query: 328
Effective length of database: 356
Effective search space:   116768
Effective search space used:   116768
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