Alignments for a candidate for Psest_0084 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Azospirillum brasilense Sp245

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate AZOBR_RS08575 AZOBR_RS08575 C4-dicarboxylate ABC transporter

Query= reanno::psRCH2:GFF84
         (674 letters)



>FitnessBrowser__azobra:AZOBR_RS08575
          Length = 698

 Score =  778 bits (2010), Expect = 0.0
 Identities = 392/660 (59%), Positives = 499/660 (75%), Gaps = 9/660 (1%)

Query: 16  RALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNGK----PFQPV 71
           +A+F +A+ FS++QI TAAF+P+SS V+R+ HVGFLLL+ F  +  R   +    P+   
Sbjct: 33  KAVFAIAVAFSLFQIWTAAFNPLSSMVVRSVHVGFLLLMTFTLFGFRQEAERRSVPWYD- 91

Query: 72  AWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIIC 131
            WLLGL  FA   Y + FE DLIQR+GD  T D++VG   I LVFEAARR+MG ALPI+C
Sbjct: 92  -WLLGLGAFALGLYHYVFEVDLIQRAGDPNTTDLIVGALTIALVFEAARRIMGWALPIMC 150

Query: 132 ALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSFL 191
            +F+ Y L G +LP  LAHRGY +DQ+++ L   TEG+YGTPT+VSAT+IFLFILFG+FL
Sbjct: 151 GVFIPYALFGRHLPFGLAHRGYDVDQVIDNLYLSTEGIYGTPTFVSATFIFLFILFGAFL 210

Query: 192 EQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKRF 251
           E+AGMIKLF D ++GL GH  GGPAKV+V+SS  MGTI GSGVANV+TTGQFTIPLM RF
Sbjct: 211 ERAGMIKLFNDVSLGLVGHAKGGPAKVAVISSGFMGTINGSGVANVLTTGQFTIPLMMRF 270

Query: 252 GYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVFW 311
           GYRPAFAG VEAT+SMG QIMPPVMGA AFIMAETI VPF +IA AA IPA+LYFGS FW
Sbjct: 271 GYRPAFAGAVEATASMGGQIMPPVMGAAAFIMAETIGVPFSDIAIAAAIPAILYFGSAFW 330

Query: 312 MVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLALT 371
           MVHLEA +  L GLPKD+CPS + A+KE WYL++PL  LV+LLFSG TP+FAG IG+ALT
Sbjct: 331 MVHLEAGKHNLVGLPKDQCPSVLGALKESWYLILPLAALVYLLFSGFTPLFAGVIGIALT 390

Query: 372 AIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGI---GVIFGVIAALVAVCWFIKG 428
             +ILG+ I+  +   ALR+ FW+ LGL+ A  +++G+    + F ++  LV  C  +KG
Sbjct: 391 VALILGTRIVGFIGPTALRVGFWVVLGLIAAALWRMGLRTEHLAFAIVGLLVLPCLALKG 450

Query: 429 GRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLS 488
           GR+TL + + +L +GA++AV VG+ACALVGV+IG+++LTG+AS+FA  I+ +   NL ++
Sbjct: 451 GRETLALLVQSLADGAKNAVGVGVACALVGVLIGILTLTGLASSFASTIMDLSGGNLLIA 510

Query: 489 LLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPVA 548
           LLLTML C+VLG G+PT  NYIIT++IAAPALL +GVPLIVSHMFVFYFGIMADLTPPVA
Sbjct: 511 LLLTMLACIVLGTGLPTTANYIITAAIAAPALLQMGVPLIVSHMFVFYFGIMADLTPPVA 570

Query: 549 LACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATLYMLFKAAF 608
           LA  AA+ I +   ++I   A R+A+AG++VPFMAVY+PALM+Q  D  A  Y+LFKA  
Sbjct: 571 LAALAASSICRAGHMEIGWIATRVAMAGYVVPFMAVYDPALMLQTDDPLAVAYVLFKALI 630

Query: 609 AVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLIQHIWRARR 668
           ++GLWGA   GY   PM   E+V A AAA   VL++P++DE GF + A FL+    R RR
Sbjct: 631 SIGLWGAATIGYFWTPMNWAERVFAAAAAFLFVLSLPVTDEAGFVMTAAFLLWQRHRLRR 690


Lambda     K      H
   0.330    0.143    0.445 

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: 1618
Number of extensions: 101
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: 674
Length of database: 698
Length adjustment: 39
Effective length of query: 635
Effective length of database: 659
Effective search space:   418465
Effective search space used:   418465
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources