GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuK in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= uniprot:A0A166QFW2
         (381 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Maltose/maltodextrin
           transport ATP-binding protein MalK (EC 3.6.3.19)
          Length = 384

 Score =  639 bits (1648), Expect = 0.0
 Identities = 326/384 (84%), Positives = 350/384 (91%), Gaps = 3/384 (0%)

Query: 1   MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60
           +IKLKLDNVNKQLGG RILRDVSLEI+AGEFVVFVGPSGCGKSTLLRLIAGLDSIC GDL
Sbjct: 1   VIKLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDL 60

Query: 61  LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120
           LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKT+K SLRERVLKTAQI
Sbjct: 61  LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQI 120

Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180
           LQLDKLLQRKP+ELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH
Sbjct: 121 LQLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180

Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240
            RLGSTMIYVTHDQVEAMTLADKIVVLNGGR+EQVGSPRELYE PASRFVAGFLGSP+MN
Sbjct: 181 GRLGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMN 240

Query: 241 FLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAG--- 297
           FL ARL +PGETS +D+ + G+T LPFDS++LA G+PL+LGIRPEH+SLKAA G+AG   
Sbjct: 241 FLPARLHSPGETSQIDSPLLGMTPLPFDSAHLAVGSPLTLGIRPEHMSLKAAQGSAGVGV 300

Query: 298 VVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVAL 357
           V V  VEYLGSETYVHLE+G+DEPLICRCEV+AGW+ GDRVEL L   ++HLFDADG AL
Sbjct: 301 VGVVGVEYLGSETYVHLESGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDADGTAL 360

Query: 358 SRHPHAIETLPAGVPLRSARASAL 381
            RHP  IE LP  VP RS +A AL
Sbjct: 361 RRHPAVIEVLPEDVPQRSPKAGAL 384


Lambda     K      H
   0.320    0.137    0.394 

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: 550
Number of extensions: 9
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: 381
Length of database: 384
Length adjustment: 30
Effective length of query: 351
Effective length of database: 354
Effective search space:   124254
Effective search space used:   124254
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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