GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Cupriavidus basilensis 4G11

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>FitnessBrowser__Cup4G11:RR42_RS28305
          Length = 472

 Score =  419 bits (1078), Expect = e-122
 Identities = 202/449 (44%), Positives = 299/449 (66%), Gaps = 5/449 (1%)

Query: 6   QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65
           ++  L RGLK+RHIQ+IA+GGAIG GLFLG+   +  AGP ++L YAIGGV  F IMR L
Sbjct: 15  EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74

Query: 66  GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125
           GE++   PV+GSF+ +A ++ G F GF +GW+YW ++V+  MAE+TAV  YVHYW+P VP
Sbjct: 75  GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134

Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG--GPQA 183
            W+ AL   A +  +N   V  +GE EFWFA+IKVV ++ MI+ G  ++  G    GP A
Sbjct: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTA 194

Query: 184 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 243
           S SNLW+HGGF P G  G+   L ++MF++ G+ELIG+TA EA  P+K +P A N V++R
Sbjct: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254

Query: 244 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 303
           ILIFY+ +L ++++L PWNE+  G SPFV +F +IG    A ++N+VV+TAA S  NSG+
Sbjct: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314

Query: 304 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 363
           ++  RMLY LA+ G APRA  +V  + VP +AI  SA      V++NY++P +    + +
Sbjct: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374

Query: 364 LVVAALVLNWALISLTHLKSRRAMVAAG--ETLVFKSFWFPVSNWICLAFMALILVILAM 421
           + +   +  W++I + HL  R+A +AAG  + + F+    P +NW+ +AFM  + V+L++
Sbjct: 375 ISLVGSLWTWSIIMIAHLGYRKA-IAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSL 433

Query: 422 TPGLSVSVLLVPLWLVVMWAGYAFKRRRA 450
            PG  V++ + P+W  ++  GY F + RA
Sbjct: 434 DPGTRVALYVAPVWFALLGIGYRFTKSRA 462


Lambda     K      H
   0.327    0.140    0.440 

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: 569
Number of extensions: 22
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: 461
Length of database: 472
Length adjustment: 33
Effective length of query: 428
Effective length of database: 439
Effective search space:   187892
Effective search space used:   187892
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 (21.7 bits)
S2: 51 (24.3 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 (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