GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Thiothrix lacustris DSM 21227

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= reanno::Smeli:SMc02121
         (258 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  145 bits (367), Expect = 9e-40
 Identities = 84/247 (34%), Positives = 143/247 (57%), Gaps = 12/247 (4%)

Query: 14  TTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKG 73
           T    + ++N++K +    VL D NL +  GE   + GPSG GK+T++R I   E+  +G
Sbjct: 2   TRSPILTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEG 61

Query: 74  KIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQV 133
           +I+++G    +D+ +I   +R    VFQ + LFPHLT+ +N         KM   + + +
Sbjct: 62  QILLNG----DDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFG----LKMAGVDVQDI 113

Query: 134 AMHFLER---VKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVK 190
           A+   +    V++ E A + P QLSGGQ+QRVAIAR++  RPKILL DE  SALD ++ +
Sbjct: 114 AVRVADALAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQ 173

Query: 191 EVLDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERT 249
           ++   +  L  + G+T + VTH+   A  +++R++ M  GQ  +  +P E +++P++   
Sbjct: 174 QMQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFV 233

Query: 250 KLFLSQI 256
             F+ +I
Sbjct: 234 AQFIGEI 240


Lambda     K      H
   0.322    0.136    0.397 

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: 224
Number of extensions: 10
Number of successful extensions: 4
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: 258
Length of database: 369
Length adjustment: 27
Effective length of query: 231
Effective length of database: 342
Effective search space:    79002
Effective search space used:    79002
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 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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