GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Brucella inopinata BO1

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_008508798.1 BIBO1_RS14845 amino acid permease

Query= uniprot:A0A0C4YRF7
         (472 letters)



>NCBI__GCF_000182725.1:WP_008508798.1
          Length = 467

 Score =  416 bits (1069), Expect = e-121
 Identities = 206/444 (46%), Positives = 297/444 (66%), Gaps = 4/444 (0%)

Query: 15  EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74
           EE  L R L +RH+Q+IAIGG IG GLF+G+G+A+++AGP ++L YAI G  +FF+MRAL
Sbjct: 15  EEPHLARNLSNRHLQLIAIGGTIGTGLFMGSGKAVSLAGPSILLIYAITGFMLFFVMRAL 74

Query: 75  GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134
           GE+LL      SFA +A +++GP A F TGW+YW  W+VT +AE+ AV+ YV +WFP + 
Sbjct: 75  GEILLSNLQYRSFADFAGDYLGPCAQFFTGWTYWLCWIVTAVAEVVAVSGYVSFWFPHLA 134

Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFG-VTPLGPT 193
            WIPAL  + +L ++N   V  FGE+EFWFALIK++TI+ +I+ G+ ++  G V P G  
Sbjct: 135 PWIPALGLITILLILNLPTVRNFGEIEFWFALIKIITIIGLIITGIYMLMTGFVLPNGTQ 194

Query: 194 ASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVW 253
           AS ++LW HGGF P G+LG +   QI +FA+ G+EL+G  A EA+NP + LP A N +  
Sbjct: 195 ASIAHLWNHGGFFPNGSLGFIAGFQISVFAFVGIELVGTAAAEAENPMRNLPKAINNIPI 254

Query: 254 RILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSG 313
           RI++FY+GAL +++ + PWN++ P  SPFV +F   G+  AA  +N VV+T+A+SS NSG
Sbjct: 255 RIVLFYIGALFVIITVTPWNQVDPNSSPFVAMFSLAGIGIAAHFINFVVLTSASSSSNSG 314

Query: 314 IFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPE--QVFVW 371
           I+ST RM+Y LA  G AP+AF ++S++ VP  A+ FS   +   V+L Y      QVF  
Sbjct: 315 IYSTSRMVYGLATVGLAPKAFSKLSNRKVPVHALIFSCIFLLSSVVLLYAGQSMIQVFTL 374

Query: 372 VTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLL 431
           VT+IS +  ++ WSII++++L YR+       K+  F+MPG   +  +V  F   V   L
Sbjct: 375 VTTISALLFIFIWSIILVSYLQYRRKHPERHEKS-TFKMPGGRASVVMVFVFFAFVLWAL 433

Query: 432 SLDPGTRVALYVAPVWFALLGIGY 455
           + +P T  A+ V P+WF LLGI Y
Sbjct: 434 TQEPDTLAAMKVTPLWFVLLGIAY 457


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: 714
Number of extensions: 40
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: 467
Length adjustment: 33
Effective length of query: 439
Effective length of database: 434
Effective search space:   190526
Effective search space used:   190526
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