GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Pantoea rwandensis LMG 26275

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter

Query= uniprot:A0A0C4YRF7
         (472 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  427 bits (1099), Expect = e-124
 Identities = 216/465 (46%), Positives = 307/465 (66%), Gaps = 5/465 (1%)

Query: 1   MTDVRKLLNEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSY 60
           M D  K    E    EK L R L +RHIQ+IAIGGAIG GLF+G+G+ I++AGP ++  Y
Sbjct: 1   MVDQSKEALIEAEQPEK-LRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 59

Query: 61  AIGGVAIFFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEIT 120
            I G  +FF+MRA+GELLL      SF+ +A + +GP+AG+ TGW+YWF WVVTG+A++ 
Sbjct: 60  MIIGFMLFFVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVV 119

Query: 121 AVAVYVHYWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGL 180
           A++ Y   WFP    W+ AL  +     +N   V +FGE+EFWFA+IK+V IVA+I+ G+
Sbjct: 120 AISAYFQLWFPGFSIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGI 179

Query: 181 AIIFFGV-TPLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQN 239
            ++     +P G TAS SN+W HGG  P G  G     QI +FA+ G+EL+G  A E ++
Sbjct: 180 VLVSMHYPSPNGTTASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKD 239

Query: 240 PEKVLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVN 299
           P KVLP A N +  RI++FYV AL+++MA+ PWN++ P  SPFV +F  IG+P AA+IVN
Sbjct: 240 PHKVLPRAINAIPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVN 299

Query: 300 LVVITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVL 359
            VV+T+AASS NSGIFST RML+ LA+ G A +AFGR+S++ VP+  + FS   + +GV 
Sbjct: 300 FVVLTSAASSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVA 359

Query: 360 LNYIVPE--QVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYAN 417
           L Y++P+   VF  VT++S +  ++ W+II+ ++L YRK     R  A  F+MP   +  
Sbjct: 360 LIYLIPDVMTVFTMVTTVSAILFMFVWTIILCSYLAYRKQ-HPQRHAASKFKMPLGKFMC 418

Query: 418 WLVVAFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRA 462
           W+ +AF   V VLL+L   TR AL V P+WF +L +G+   + +A
Sbjct: 419 WVCMAFFAFVLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRKA 463


Lambda     K      H
   0.328    0.142    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: 716
Number of extensions: 35
Number of successful extensions: 4
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: 472
Length of database: 463
Length adjustment: 33
Effective length of query: 439
Effective length of database: 430
Effective search space:   188770
Effective search space used:   188770
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: 51 (24.3 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