GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_03050 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate H281DRAFT_00223 H281DRAFT_00223 amino acid ABC transporter membrane protein 1, PAAT family

Query= reanno::pseudo3_N2E3:AO353_03050
         (229 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00223 H281DRAFT_00223 amino
           acid ABC transporter membrane protein 1, PAAT family
          Length = 229

 Score =  255 bits (651), Expect = 6e-73
 Identities = 126/228 (55%), Positives = 172/228 (75%), Gaps = 1/228 (0%)

Query: 2   LKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPD 61
           L+GYG ++L+G W T++LA+ S+ALA +LGL+G A +LS  R+    G +Y+T++RG+PD
Sbjct: 3   LQGYGPLLLNGTWQTVKLAVLSLALAFLLGLVGAAAKLSKNRFSHGAGTVYTTLVRGVPD 62

Query: 62  LVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIP 121
           LVL+LL+FY  Q  LN +  LLG+D  ID++P VAG+  LGFI+GAY +ETFRGAF+A+P
Sbjct: 63  LVLMLLLFYSIQIWLNNLTDLLGWDQ-IDIDPFVAGVAVLGFIYGAYFTETFRGAFLAVP 121

Query: 122 KGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181
           +GQ EAGAAYGM+S+QVF R++ PQM+R A+PG  NNW V+ KATAL+S++GL D++  +
Sbjct: 122 RGQLEAGAAYGMTSWQVFSRIMFPQMMRFALPGIGNNWQVMVKATALVSIIGLADVVKAS 181

Query: 182 KQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL 229
           + A   T   F F L   A+YLVIT+VS   L +LEKRYS GVR ADL
Sbjct: 182 QDAGKGTLRFFFFTLFAGAIYLVITTVSNFVLMYLEKRYSTGVRKADL 229


Lambda     K      H
   0.329    0.144    0.421 

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: 209
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: 229
Length of database: 229
Length adjustment: 23
Effective length of query: 206
Effective length of database: 206
Effective search space:    42436
Effective search space used:    42436
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: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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