GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Marivita geojedonensis DPG-138

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_050931869.1 MGEO_RS07795 ABC transporter permease subunit

Query= reanno::pseudo1_N1B4:Pf1N1B4_3433
         (232 letters)



>NCBI__GCF_002115805.1:WP_050931869.1
          Length = 228

 Score =  164 bits (415), Expect = 1e-45
 Identities = 81/218 (37%), Positives = 138/218 (63%), Gaps = 4/218 (1%)

Query: 12  LPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQL 71
           L L+  GL  T+ L AL +FFG   A+P+   R+S   +++ +A+ + Y++RGTP+LVQ+
Sbjct: 9   LELWRIGLTNTVMLTALGVFFGFFVAIPIAAARLSSNKLLSKAAFGYVYIVRGTPLLVQI 68

Query: 72  FLIYYGLAQFEAVRESF-LWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEA 130
           F+IYYGL QF    ++  +W +   A  C  LAF +N++AY +EI+ G + A P G IEA
Sbjct: 69  FIIYYGLGQFHKELKAIGVWWFFRDAFNCGLLAFTLNSAAYQSEILRGGILAVPKGVIEA 128

Query: 131 AKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQ 190
             A+G++ +++++RI++P  + R LP + NE++++L+ +SL SI+T+ D+ G AR + AQ
Sbjct: 129 GSALGLTTLQIFRRIIMPITVGRMLPAFGNELVLLLKASSLVSIITVRDVLGQARFIYAQ 188

Query: 191 FYLPFEAYITAGVFYLCLTFILVRLFKMAEHR--WLGY 226
            +     +  A + YL +  I+  +++  E R  WL Y
Sbjct: 189 TF-DLSVFYIAALNYLIVVMIIEAIWRRLERRNAWLKY 225


Lambda     K      H
   0.330    0.140    0.427 

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: 119
Number of extensions: 5
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: 232
Length of database: 228
Length adjustment: 23
Effective length of query: 209
Effective length of database: 205
Effective search space:    42845
Effective search space used:    42845
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 (21.9 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