GapMind for catabolism of small carbon sources

 

Aligments for a candidate for potD in Pseudomonas fluorescens FW300-N2E3

Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate AO353_08580 AO353_08580 spermidine/putrescine ABC transporter substrate-binding protein

Query= SwissProt::Q02UB7
         (367 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_08580 AO353_08580
           spermidine/putrescine ABC transporter substrate-binding
           protein
          Length = 364

 Score =  540 bits (1392), Expect = e-158
 Identities = 266/366 (72%), Positives = 309/366 (84%), Gaps = 2/366 (0%)

Query: 2   MKRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYD 61
           +K+ GKTLLAL+L G +AG AQA D+KVLHVYNWSDYIAPDT+  F KE+GIKVVYDV+D
Sbjct: 1   LKKTGKTLLALSLMGVMAGAAQA-DDKVLHVYNWSDYIAPDTIANFEKESGIKVVYDVFD 59

Query: 62  SNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVS 121
           SNE LEAKLLAGKSGYDVVVPSN+FLAKQIKAGVYQ+LDKSKL N+ NLNK L+  + VS
Sbjct: 60  SNETLEAKLLAGKSGYDVVVPSNNFLAKQIKAGVYQELDKSKLTNYGNLNKSLLKAVSVS 119

Query: 122 DPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSP 181
           DP N+HA PYMWG+IGIGYN +KVKAA G +  +DSWD+V KPENI KLK CGVSFLDSP
Sbjct: 120 DPDNKHAFPYMWGSIGIGYNAEKVKAALGIDK-IDSWDVVLKPENIAKLKSCGVSFLDSP 178

Query: 182 TEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGY 241
           TE+LP ALHYLG   D+   ++LK AEELFLKIRP +TYFHSSKYISDLANGNICVA+GY
Sbjct: 179 TEMLPVALHYLGLPTDSQKKEDLKKAEELFLKIRPSITYFHSSKYISDLANGNICVAVGY 238

Query: 242 SGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEI 301
           SGD+ QAK+RA EA +KV V Y IPKEGAGSF+DMVAIPKDAEN EGA  F+N+L++P++
Sbjct: 239 SGDVQQAKTRAAEAGDKVKVSYAIPKEGAGSFYDMVAIPKDAENVEGAYKFMNYLLQPKV 298

Query: 302 MAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWT 361
           MAEIT+ V+FPNGNA AT  V++ I +DPGIYP+ +V  KLY   DLPA TQR +TRSWT
Sbjct: 299 MAEITNAVRFPNGNAEATQYVNKDITSDPGIYPTADVQSKLYAIADLPAATQRELTRSWT 358

Query: 362 KIKSGK 367
           KIKSGK
Sbjct: 359 KIKSGK 364


Lambda     K      H
   0.315    0.133    0.390 

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: 559
Number of extensions: 16
Number of successful extensions: 3
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: 367
Length of database: 364
Length adjustment: 30
Effective length of query: 337
Effective length of database: 334
Effective search space:   112558
Effective search space used:   112558
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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