GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Cronobacter universalis NCTC 9529

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_007700807.1 AFK65_RS15775 ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_001277175.1:WP_007700807.1
          Length = 375

 Score =  302 bits (774), Expect = 9e-87
 Identities = 166/375 (44%), Positives = 236/375 (62%), Gaps = 12/375 (3%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA +    + K Y  G    +  I+L I +GEF+++VGPSGC KST +  +AGLETI+GG
Sbjct: 1   MAEVIFNKLEKVYSNGFK-AVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGG 59

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            + IG++ V+ ++PK+R IAMVFQ+YALYP M+VREN+ FGLK+ K+P+  I+ +V   A
Sbjct: 60  EVRIGEKLVNNLAPKERGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQINRQVDEAA 119

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           K+L++E LL+R P QLSGGQ QRVA+GRA+ ++P ++LFDEPLSNLDAKLR  MR  +  
Sbjct: 120 KILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISD 179

Query: 181 MHQRLK-----TTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASF 235
           +H++LK      TTVYVTHDQ EAMT+GD++ VMK G I Q  TP  +Y+ P N FVA F
Sbjct: 180 LHKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHYPKNMFVAGF 239

Query: 236 IGSPPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAA 295
           IG+P MN  P +L  + G+L+  +   +           A    + V  G+RPE I ++ 
Sbjct: 240 IGAPEMNIKPGKLVEEAGQLLICIGDNRLALTPRQQEKVAAYAGQQVFFGIRPEYISISD 299

Query: 296 GEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVA-PQVGETL----TLQFD 350
                       V+V E  G +  V++++ D ++ CR+  D A P + + L      +FD
Sbjct: 300 TPYAEPCGAGELVRV-ENMGHEFFVYLKVADFEMTCRIPSDEAKPMIDKGLHRKVYFKFD 358

Query: 351 PSKVLLFDANTGERL 365
            +K  LFDA T + L
Sbjct: 359 MNKCHLFDAKTEQNL 373


Lambda     K      H
   0.318    0.135    0.382 

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: 394
Number of extensions: 12
Number of successful extensions: 3
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: 386
Length of database: 375
Length adjustment: 30
Effective length of query: 356
Effective length of database: 345
Effective search space:   122820
Effective search space used:   122820
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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