GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Pseudomonas fluorescens FW300-N1B4

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  313 bits (802), Expect = 5e-90
 Identities = 173/362 (47%), Positives = 223/362 (61%), Gaps = 10/362 (2%)

Query: 15  GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74
           GG  +L  + L I  GEFVV +GPSGCGKST+LR+IAGL+ I GG L I G  VNDL  R
Sbjct: 14  GGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPR 73

Query: 75  ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134
           ER V MVFQ+YALYPHMSVYDNI+FGL+  K     +  RV + A +L L+ LL+RKP+ 
Sbjct: 74  ERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKE 133

Query: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194
           +SGGQ+QR A+ RA+ + P + LFDEPLSNLDA LR Q+R +I RLH RL +T +YVTHD
Sbjct: 134 LSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHD 193

Query: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254
           Q+EAMTLAD+++++  GR+ Q GSP ELY  P + F AGF+G+P MNFLS  +Q      
Sbjct: 194 QVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETS 253

Query: 255 FIETAHQRWALTGERF--SRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEIL 312
            ++T    W +T   F  S L     + L +RP+HV +      AA  T  V V  VE L
Sbjct: 254 LVDTL--VWGITSLPFDSSNLAAGTPLSLGIRPEHVSL-----KAADGTAGVVVTAVEYL 306

Query: 313 GADALLTTRCG-DQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENLSLPDAALT 371
           G++  +    G D+ L          Q G  + L LD   LH+FD +       P A  T
Sbjct: 307 GSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALSRHPHAIET 366

Query: 372 AP 373
            P
Sbjct: 367 LP 368


Lambda     K      H
   0.321    0.137    0.403 

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: 422
Number of extensions: 21
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: 406
Length of database: 381
Length adjustment: 31
Effective length of query: 375
Effective length of database: 350
Effective search space:   131250
Effective search space used:   131250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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