GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5402 in Pseudomonas simiae WCS417

Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate GFF4561 PS417_23345 amino acid ABC transporter substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5402
         (343 letters)



>FitnessBrowser__WCS417:GFF4561
          Length = 342

 Score =  542 bits (1396), Expect = e-159
 Identities = 262/343 (76%), Positives = 305/343 (88%), Gaps = 1/343 (0%)

Query: 1   MKLLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVG 60
           M   K+TLA + A AVLG++  A+AG TLDA+QKKGF+QCGVSDGLPGF VPDS GK+ G
Sbjct: 1   MNPFKTTLAAIGATAVLGLASTAEAGTTLDAIQKKGFIQCGVSDGLPGFGVPDSKGKMTG 60

Query: 61  IDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKF 120
           ID D C AVAAAVFGDA+KVKF+QL AKERFTALQSGEID++SRN+T TSSRD+GMGL F
Sbjct: 61  IDVDVCHAVAAAVFGDASKVKFTQLTAKERFTALQSGEIDLISRNTTWTSSRDSGMGLVF 120

Query: 121 PGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFD 180
            G +TYYDGIGFL NNKLGV +AK+LDGAT+CIQAGTTTELNVSDYFR +G+KYTPITFD
Sbjct: 121 TG-VTYYDGIGFLVNNKLGVTAAKQLDGATVCIQAGTTTELNVSDYFRTHGMKYTPITFD 179

Query: 181 TSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEW 240
           T+DESAK LE+GRCDVLT+D+S L+AQR K+A P ++VVLPE ISKEPLGP+VR GDDEW
Sbjct: 180 TADESAKGLEAGRCDVLTTDQSGLYAQRIKMAQPDEFVVLPEVISKEPLGPLVRKGDDEW 239

Query: 241 LAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQI 300
            +IV+WT +A+LNAEE G+TS+NVE +AK+TKNPDVAR+LGADGEYGKDLKL KDWVVQI
Sbjct: 240 FSIVKWTLFAMLNAEEMGITSQNVEEQAKTTKNPDVARLLGADGEYGKDLKLRKDWVVQI 299

Query: 301 VKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343
           VKQVGNYGE+FERN+G+G+ L+I RGLNALWN GGIQYAPPVR
Sbjct: 300 VKQVGNYGEVFERNIGQGSVLKIKRGLNALWNNGGIQYAPPVR 342


Lambda     K      H
   0.315    0.133    0.383 

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: 488
Number of extensions: 15
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: 343
Length of database: 342
Length adjustment: 29
Effective length of query: 314
Effective length of database: 313
Effective search space:    98282
Effective search space used:    98282
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: 42 (22.0 bits)
S2: 49 (23.5 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