GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Acidovorax sp. GW101-3H11

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3200
          Length = 604

 Score =  241 bits (614), Expect = 3e-68
 Identities = 128/250 (51%), Positives = 169/250 (67%), Gaps = 12/250 (4%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           + I  ++K YG   VL+D+ LTV  G   VI GPSGSGKST++R IN LE    G I +D
Sbjct: 356 VTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAID 415

Query: 83  GIELTSDLKNID-----------KVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131
           G EL    ++ D           K R +VGMVFQ+FNLFPHLT+LEN+  AP+ VRK+ +
Sbjct: 416 G-ELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLAR 474

Query: 132 REAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPE 191
            EAE  A+  L +V + ++A  YP QLSGGQQQRVAIAR+L +KPK++LFDEPTSALDPE
Sbjct: 475 AEAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDPE 534

Query: 192 MIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSE 251
           ++ EVLD + +LA  G T++ VTHE+GFA+ VA+ V+FM  G++VE   P   F  P   
Sbjct: 535 LVGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDHP 594

Query: 252 RTKQFLSQIL 261
           RT  FL+++L
Sbjct: 595 RTAAFLAKVL 604


Lambda     K      H
   0.320    0.134    0.391 

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: 306
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: 263
Length of database: 604
Length adjustment: 31
Effective length of query: 232
Effective length of database: 573
Effective search space:   132936
Effective search space used:   132936
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:

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