GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830
          Length = 361

 Score =  246 bits (628), Expect = 7e-70
 Identities = 151/362 (41%), Positives = 209/362 (57%), Gaps = 13/362 (3%)

Query: 4   LELRNVNKTYG--PGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGA 61
           +E+RNV+K Y   PGL   L N+ + I D EF  L+GPSGCGK+TL+  IAG E +S G 
Sbjct: 7   IEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSDGE 66

Query: 62  ILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121
           I +    ++ + P  R +  VFQSYAL+P MSV  NIAFGL+++ +    I + V  +  
Sbjct: 67  IRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEMLA 126

Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181
           L+Q++HL  RKP +LSGGQQQRVA+ RALA +PK+ L DEPLS LD KLR EM+ E+K +
Sbjct: 127 LVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELKRV 186

Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241
            +    T ++VTHDQ EA+TL D++AVM  G I Q G+P +IY  P + FVA FIG   +
Sbjct: 187 QKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIGD--I 244

Query: 242 NFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGL 301
           NF+P  ++R        + +G    E+P   Q  G +  +V L  RPE+  L   E    
Sbjct: 245 NFLPGHIKRGQQNEKLFVPNGMP-VEIPCPAQ--GFDGSKVQLAFRPERSQLV--EPTQP 299

Query: 302 PTIRAEVQVTEPTGPDTLVFVNL-NDTKVCCR---LAPDVAPAVGETLTLQFDPAKVLLF 357
             +R  ++     G  TL    L ND KV  R      +    VG+ + +   P   LL 
Sbjct: 300 HHLRGVIEAVLYVGTATLYQCRLNNDIKVMLRENNEGLNHGRVVGDRVAVNLPPHACLLM 359

Query: 358 DA 359
           +A
Sbjct: 360 EA 361


Lambda     K      H
   0.319    0.138    0.393 

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: 383
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: 386
Length of database: 361
Length adjustment: 30
Effective length of query: 356
Effective length of database: 331
Effective search space:   117836
Effective search space used:   117836
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 (21.7 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