GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Paenisporosarcina indica PN2

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_075618804.1 GY23_RS08645 amino acid ABC transporter permease

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



>NCBI__GCF_001939075.1:WP_075618804.1
          Length = 218

 Score =  105 bits (262), Expect = 7e-28
 Identities = 76/217 (35%), Positives = 120/217 (55%), Gaps = 18/217 (8%)

Query: 9   ILDGAWLTLQLALSSMALAIVLGLI---GVALRLSPIRWLARLGDLYSTVIRGIPDLVLI 65
           +L+GA +T+ L L ++  +I LG I   GV      + WLA+    Y  ++RG P L+ +
Sbjct: 12  MLEGAKVTILLFLIAIVSSIPLGFILTLGVKSNNKIVSWLAQT---YIYLMRGTPLLLQL 68

Query: 66  LLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFI--FGAYLSETFRGAFMAIPKG 123
           L I +G   L     P++G  +Y+ L+  VA    LGFI  + AY +E FRG  +AI KG
Sbjct: 69  LFICFGLPLL-----PVVG--EYLVLDRFVAAC--LGFILNYAAYFAEIFRGGLLAIDKG 119

Query: 124 QAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQ 183
           Q EA    G++ +Q   R+++PQM R+A+P  +N  + L K TAL+  V + +++  A+ 
Sbjct: 120 QYEASHVLGLNKWQTTTRIILPQMFRIALPAISNESVTLVKDTALLYAVAVPELLHFAQT 179

Query: 184 AADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRY 220
           A +       FF A   +YL IT V  +  + LE+R+
Sbjct: 180 AVNRDFTVVPFFFA-GMIYLAITLVLTMFFKWLERRF 215


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: 166
Number of extensions: 13
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: 218
Length adjustment: 22
Effective length of query: 207
Effective length of database: 196
Effective search space:    40572
Effective search space used:    40572
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 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