GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5404 in Azospirillum brasilense Sp245

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS15680 AZOBR_RS15680 amino acid
           ABC transporter permease
          Length = 216

 Score =  118 bits (295), Expect = 2e-31
 Identities = 75/222 (33%), Positives = 125/222 (56%), Gaps = 28/222 (12%)

Query: 144 VFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRG 203
           +F L AV   QW     TL ++ +  +G   +G+V+AL R S++ A+R+    +I+ ++G
Sbjct: 10  LFLLSAV---QW-----TLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQG 61

Query: 204 VPLITVLFM----SSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKG 259
            PL+  LF+    ++VM       G++ +    A +G+ L  SA++ E+ RG +QA+P+G
Sbjct: 62  TPLLMQLFLVFFGATVM-------GLDLNPWAAAALGLTLNASAFLGEIWRGCIQAVPRG 114

Query: 260 QYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNS--- 316
           Q+EAA+A+GL Y   M  VILPQA+K+ +P  V   + L K TSL  IIG  +L  +   
Sbjct: 115 QWEAASALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQI 174

Query: 317 VKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERK 358
           V  A   P  +      +   A+++++ C+ +S  S  LER+
Sbjct: 175 VNNATFQPFLV------FGIVAVLYFLMCWPLSLLSARLERR 210


Lambda     K      H
   0.330    0.144    0.469 

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: 263
Number of extensions: 17
Number of successful extensions: 3
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: 365
Length of database: 216
Length adjustment: 26
Effective length of query: 339
Effective length of database: 190
Effective search space:    64410
Effective search space used:    64410
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: 47 (22.7 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