GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5403 in Lactobacillus silagei IWT126

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_054653756.1 CES79_RS00815 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>NCBI__GCF_002217945.1:WP_054653756.1
          Length = 212

 Score = 92.0 bits (227), Expect = 1e-23
 Identities = 51/126 (40%), Positives = 79/126 (62%), Gaps = 3/126 (2%)

Query: 247 TLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTS 306
           T+ LT+YT+AFIAE VRSGI+SV  GQ E AR+ GL     +R +++PQA R +IPPL +
Sbjct: 89  TIGLTIYTSAFIAETVRSGIQSVDPGQMEGARANGLSFWQAMRYIVLPQAFRYVIPPLGN 148

Query: 307 QYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSV-YLAISISISLLMNW 365
           Q++NL KNSS+ A +   ++  ++ G V+           I + + YL I++ +S  M +
Sbjct: 149 QFINLVKNSSVLAFVAGFDL--MYQGNVIASDSLNTMSTYICIGILYLIITLPLSYWMRY 206

Query: 366 YNKRIA 371
             K++A
Sbjct: 207 LEKKLA 212



 Score = 45.1 bits (105), Expect = 2e-09
 Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 2/92 (2%)

Query: 61  SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120
           +Y  + L G   TLL + I ++ + I+G +  +   +    +  +A +Y+EVFRNIP L+
Sbjct: 7   NYGSLLLQGFGQTLLCSVIALVFSLIIGSMFAIFETTPIKALRVIARIYIEVFRNIPLLV 66

Query: 121 QILFWYFAV--FLSMPGPRAAHNFGDTFFVSS 150
             +F++  +  F++      A   G T + S+
Sbjct: 67  ITMFFFVVIPMFITKINGFTAGTIGLTIYTSA 98


Lambda     K      H
   0.328    0.141    0.430 

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: 198
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 375
Length of database: 212
Length adjustment: 26
Effective length of query: 349
Effective length of database: 186
Effective search space:    64914
Effective search space used:    64914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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