GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Pseudomonas fluorescens FW300-N2E3

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate AO353_03380 AO353_03380 sugar ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03380
          Length = 386

 Score =  273 bits (698), Expect = 6e-78
 Identities = 164/379 (43%), Positives = 232/379 (61%), Gaps = 32/379 (8%)

Query: 1   MGQIQLTDLTKRFGDTV--AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSG 58
           M  ++L ++ K +G  +   + ++ L IDD EFL+LVGPSGCGKST +  +AGLE  + G
Sbjct: 1   MATLELRNVNKTYGSGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLENISGG 60

Query: 59  DIYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEV 118
            I +    ++   P++RDIAMVFQ YALYP M+VR NI FGL+  +   +AE DE V  V
Sbjct: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRK-MPAAEIDEEVARV 119

Query: 119 AETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 178
           A+ L I  LL RKP +LSGGQQQRVA+GRA+ R P+++L DEPLSNLDAKLR EMRTE++
Sbjct: 120 AKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179

Query: 179 NLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEP 238
            +  +L  TTVYVTH+Q EAMT+ D++AVM DG +QQ  +P + Y++P NLFVA FIG P
Sbjct: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKQIYNDPANLFVASFIGSP 239

Query: 239 MINLV--RGTRSESTFVG------EHFSYPLD-EDVMESVDDRDDFVLGVRPEDIEVADA 289
            +N +  R  R +   +            PL  +D    ++DR + +LG+RPE I +A+ 
Sbjct: 240 PMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDA--GLEDR-EVILGMRPEQIVLANG 296

Query: 290 APDDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQP----SADDALQAVTEGMHLVTRGD 345
             +        ++ +V V EP G   ++ ++  +       A D   AV         G+
Sbjct: 297 EANGLP----TIRAEVQVTEPTGPDTLVFVNLNETKVCCRLAPDVAPAV---------GE 343

Query: 346 RVTVTIPPDKIHLFDAETG 364
            +T+   P K+ LFDA+TG
Sbjct: 344 TLTLQFDPSKVLLFDAKTG 362


Lambda     K      H
   0.317    0.135    0.386 

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: 388
Number of extensions: 15
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: 383
Length of database: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
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: 41 (21.6 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