GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlE in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-sorbitol, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_5038 Various polyols ABC transporter, periplasmic substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_1963
         (436 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5038 Various polyols ABC
           transporter, periplasmic substrate-binding protein
          Length = 436

 Score =  763 bits (1969), Expect = 0.0
 Identities = 367/433 (84%), Positives = 398/433 (91%)

Query: 3   ITNALILSTGLSFALASHAAETLTIATVNNGDMIRMQRLSKVFEQQHPDIKLSWVVLEEN 62
           I +A  LS GLS AL   AAET+TIATVNN DMIRMQRLSK FEQQHPD+KL+WVVLEEN
Sbjct: 4   IPSAFFLSAGLSSALLCQAAETVTIATVNNSDMIRMQRLSKTFEQQHPDVKLNWVVLEEN 63

Query: 63  VLRQRLTTDIATQGGQFDVLTIGTYETPMWGAKNWLEPMKDLPAGYDVDDIFPAVRQGLS 122
           VLRQRLTTDIATQGGQFDVLTIGTYETP+WGAK+WLEPMKDLPA YD++DIFP+VRQGLS
Sbjct: 64  VLRQRLTTDIATQGGQFDVLTIGTYETPLWGAKHWLEPMKDLPASYDLEDIFPSVRQGLS 123

Query: 123 VNDTLYALPFYGESTITYYRTDLFKAAGLTMPAQPTWSQLGEFAAKLNDPSKDQYGMCLR 182
           VNDTLYALPFYGESTITYYRTDLFK AGL+MP  PTW+QLGEFA KL+ P K+QYGMCLR
Sbjct: 124 VNDTLYALPFYGESTITYYRTDLFKNAGLSMPEHPTWTQLGEFAGKLHQPDKEQYGMCLR 183

Query: 183 GKAGWGENMALLTTMANAFGARWFDEKWQPELNGPEWKAAATFYVDTLKKYGPPGVSSNG 242
           GKAGWGENMALLTTM+NAFGARWF+E+WQP+L GPEW AAA FYV+TLK+YGPPGVSSNG
Sbjct: 184 GKAGWGENMALLTTMSNAFGARWFNEQWQPQLTGPEWTAAANFYVNTLKQYGPPGVSSNG 243

Query: 243 FNETLALFNSGKCAIWVDASVAGSFTTDKEQSRVVDSVGFAPAPTEVTDKGSSWLYAWSL 302
           FNETLALFNSGKCAIWVDASVAGSF TD  QS+V D VGF  APT+VTDKGSSWLYAWSL
Sbjct: 244 FNETLALFNSGKCAIWVDASVAGSFITDTTQSKVADKVGFVAAPTQVTDKGSSWLYAWSL 303

Query: 303 AIPATSKHKEAAKSFVTWATSKEYIQLVTDKDGITNVPPGTRISTYSDAYLKAAPFAQVT 362
           AIPATSKHKEAAK+FVTWATSK+YIQLV DKDGITNVPPGTR+STYS+AYL+AAPFA VT
Sbjct: 304 AIPATSKHKEAAKAFVTWATSKDYIQLVADKDGITNVPPGTRMSTYSNAYLQAAPFASVT 363

Query: 363 LQMMKHADPSQPSAKPVPYVGIQYVVIPEFQSIGTSVGKLFSAALTGQMSVEQALASAQS 422
           L+MM+HADP+ PS +PVPYVGIQYV IPEFQ+IGTSVGKL SAALTGQM VEQALASAQ 
Sbjct: 364 LKMMQHADPAHPSVQPVPYVGIQYVTIPEFQAIGTSVGKLLSAALTGQMPVEQALASAQQ 423

Query: 423 TTEREMKRAGYPK 435
           TTEREMKRAGYPK
Sbjct: 424 TTEREMKRAGYPK 436


Lambda     K      H
   0.315    0.130    0.391 

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: 744
Number of extensions: 14
Number of successful extensions: 1
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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