GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Streptacidiphilus oryzae TH49

Align Lactate utilization protein A (characterized)
to candidate WP_037571239.1 BS73_RS10145 (Fe-S)-binding protein

Query= SwissProt::O07020
         (238 letters)



>NCBI__GCF_000744815.1:WP_037571239.1
          Length = 251

 Score =  230 bits (586), Expect = 2e-65
 Identities = 120/244 (49%), Positives = 152/244 (62%), Gaps = 7/244 (2%)

Query: 1   MKVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMK 60
           M+V+LF+TC+ D      G+A V LLERLG EVDFP GQ CCGQP +N+GY    +  ++
Sbjct: 1   MRVALFLTCVNDAVHPRTGRAVVALLERLGVEVDFPAGQTCCGQPQFNTGYRRATEPLVR 60

Query: 61  RMIETFQDSEYVVSPSGSCTTMFRE-YPHLFQD------DPKWADKAKKLADKTYELTDF 113
           RM E F+D EYVVSPSGSC  M R+ YP +             AD A +L  +  ELT+F
Sbjct: 61  RMDEVFRDYEYVVSPSGSCAAMVRDNYPRIGAKAMAEGRGSALADAAGRLVPRVLELTEF 120

Query: 114 IVNVLGVEDVGATLHTKATLHTSCHMTRLLGVRKEPMKLLSHVKGLQFTELPGKHNCCGF 173
           +V+VLGVEDVGA      T H SCH  R+L +   P++LL  VKG+   ELPG   CCGF
Sbjct: 121 LVDVLGVEDVGAYYPHSVTYHPSCHGLRMLRLGDRPLRLLRRVKGIDLRELPGAEECCGF 180

Query: 174 GGTFSVKMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKVMHIAE 233
           GGTFSVK   +S  M  +K      TGAE L GAD  CL++IGG L R D  ++ +H+AE
Sbjct: 181 GGTFSVKNPDVSAAMGADKARNALSTGAEALCGADNSCLLHIGGTLRRADAPMRTVHLAE 240

Query: 234 VLNS 237
           +L S
Sbjct: 241 ILAS 244


Lambda     K      H
   0.321    0.136    0.411 

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: 226
Number of extensions: 8
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: 238
Length of database: 251
Length adjustment: 24
Effective length of query: 214
Effective length of database: 227
Effective search space:    48578
Effective search space used:    48578
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: 46 (22.3 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