GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Pseudomonas simiae WCS417

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>FitnessBrowser__WCS417:GFF4342
          Length = 473

 Score =  619 bits (1595), Expect = 0.0
 Identities = 301/456 (66%), Positives = 357/456 (78%), Gaps = 9/456 (1%)

Query: 10  LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69
           LKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAFMIMRQLGEM+
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70

Query: 70  AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129
            +EPVAGSFSHFA+KYWG F GFLSGWN W+LY+LV M+ELTAVG YVHYWWP +PTWVS
Sbjct: 71  VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIPTWVS 130

Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASISNLW 189
           A   F  IN INLANVK +GE EFWFAIIKVVA++GMI  G YLLVSG GGPQAS++NLW
Sbjct: 131 AAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGPQASVTNLW 190

Query: 190 SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIFYI 249
            HGGFFPHG  GL   +A+IMFSFGGLE++G TAAEAD+P+  IPKA+NQVIYRILIFYI
Sbjct: 191 EHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRILIFYI 250

Query: 250 CSLAVLLSLYPWNEVAA---------GGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300
            +L VLLSL PW+ + A          GSPFV +FS +GS   A++LN VVLTAALSVYN
Sbjct: 251 GALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALSVYN 310

Query: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360
           SG Y NSRML G+AEQG+AP+AL K+D+RGVP  +I  SA  T   V++NYLIP  AL L
Sbjct: 311 SGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQHALEL 370

Query: 361 LMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420
           LM+LVVA LV+NWA+IS +H K R+ M   G+  +FK+ W+P  N++CLAF+  ILVI+ 
Sbjct: 371 LMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPLFKALWYPYGNYVCLAFVVFILVIML 430

Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAA 456
           M PG+ VSV  +P+W++ M   Y  K +R+A    A
Sbjct: 431 MIPGIQVSVFAIPVWVMFMAVCYGIKNKRSAQQALA 466


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: 646
Number of extensions: 23
Number of successful extensions: 2
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: 473
Length adjustment: 33
Effective length of query: 428
Effective length of database: 440
Effective search space:   188320
Effective search space used:   188320
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