GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS16715
          Length = 361

 Score =  340 bits (873), Expect = 3e-98
 Identities = 183/367 (49%), Positives = 248/367 (67%), Gaps = 11/367 (2%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA++++R V K +G+     ++ +++ I +GEF +LVGPSGCGKSTL+  +AGLE ITGG
Sbjct: 1   MASVQIRAVKKQFGS--TQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I+IG   V+ + PKDRDIAMVFQ+YALYP M+VR+N+ F L + K  +A +D  V + A
Sbjct: 59  EILIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
            +L +  LL+R P QLSGGQ+QRVAMGRA+ R P+++LFDEPLSNLDAKLRV+MRTE+K 
Sbjct: 119 DILGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKE 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +HQRLKTT++YVTHDQIEAMT+ D++ VM+DG+++Q G P ++Y+ PAN FVA FIGSP 
Sbjct: 179 LHQRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPA 238

Query: 241 MNFVPLRLQRK-DGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIML-AAGEG 298
           MNF+P  L+R   G  V   D    R          G + + V  G+RPE + + AAG+G
Sbjct: 239 MNFIPATLRRNATGAEVEFADG--TRVPAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQG 296

Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358
                I  +V V EPTG DT VF +  DT +            G+ + L  D S+  LFD
Sbjct: 297 -----IATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFD 351

Query: 359 ANTGERL 365
           A +G+ L
Sbjct: 352 AESGKSL 358


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: 377
Number of extensions: 9
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: 386
Length of database: 361
Length adjustment: 30
Effective length of query: 356
Effective length of database: 331
Effective search space:   117836
Effective search space used:   117836
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 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