GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malE_Aa in Hafnia paralvei ATCC 29927

Align Maltodextrin-binding protein (characterized, see rationale)
to candidate WP_061059304.1 M988_RS19105 maltose/maltodextrin ABC transporter substrate-binding protein MalE

Query= uniprot:Q9RHZ6
         (427 letters)



>NCBI__GCF_001655005.1:WP_061059304.1
          Length = 396

 Score =  175 bits (443), Expect = 3e-48
 Identities = 127/404 (31%), Positives = 206/404 (50%), Gaps = 20/404 (4%)

Query: 28  TSNGGQNTSPSTSSSSAKGEASALPKGQTITVWSWQTGPE-LQDVKQIAAQWAKAHGDKV 86
           T   G  T   ++ ++    +SA  K +   +  W  G +    + +I  ++ K  G KV
Sbjct: 2   TKKSGIRTLALSALATLVLSSSAFAKIEEGKLVIWINGDKGYNGLAEIGKKFEKETGIKV 61

Query: 87  IVVDQSSNPKGFQFYATAARTGKGPDVVFGMPHDNNGVFAEEGLMAPV-PSGVLNTGLYA 145
           +V       K  + Y   A TG GPD++F   HD  G +A+ GL+A + PS      LY 
Sbjct: 62  LVEHPD---KLEEKYPQVAATGDGPDIIF-WAHDRFGGYAQSGLLAEIHPSKAFQDKLY- 116

Query: 146 PNTIDAIKVNGTMYSVPVSVQVAAIYYNKKLVPQPPQTWAEFV---KDANAHG---FMYD 199
           P T DA++ NG + + PV+V+  ++ YNK ++P+PP+TW E     K+  A G    M++
Sbjct: 117 PFTWDAVRYNGKLIAYPVAVEALSLIYNKDILPEPPKTWEEIPALDKELRAKGKSAIMWN 176

Query: 200 QANLYFDYAIIGGYGGYVFKDNNGTLDPNNIGLDTPGAVQAYTLMRDMVSKYHWMTPSTN 259
               YF + II   GGY FK +NGT +  ++G++  G+      + D+V   H +   T+
Sbjct: 177 LQEPYFTWPIIAADGGYAFKYDNGTYNIKDVGVNNAGSQAGLQFIVDLVKNKH-INADTD 235

Query: 260 GSIAKAEFLAGKIGMYVSGPWDTADIEKAKIDFGVTPWPTLPNGKHATPFLGVITAFVNK 319
            SIA+A F  G+  M ++GPW  ++I+K+ I++GV   PT   G  + PF+GV++A +N 
Sbjct: 236 YSIAEAAFNKGQTAMTINGPWAWSNIDKSNINYGVALLPTF-KGHPSKPFVGVLSAGINA 294

Query: 320 ES--KTQAADWSLVQALTSAQAQQMYFRDSQQIPALLSVQRSSAVQSSPTFKAFVEQLRY 377
            S  K  A ++     +T+A  +Q+         AL S Q +  ++  P   A ++  + 
Sbjct: 295 ASPNKELATEFLENYLMTNAGLEQINKDKPLGAVALKSYQET--LEKDPKIAATMQNAQK 352

Query: 378 AVPMPNIPQMQAVWQA-MSILQNIIAGKVSPEQGAKDFVQNIQK 420
              MPNIPQM A W A  S + N + G+ S ++      Q I K
Sbjct: 353 GEIMPNIPQMSAFWYAERSAIINAVNGRQSVKEALTGAEQRITK 396


Lambda     K      H
   0.315    0.130    0.392 

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: 440
Number of extensions: 32
Number of successful extensions: 6
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: 427
Length of database: 396
Length adjustment: 31
Effective length of query: 396
Effective length of database: 365
Effective search space:   144540
Effective search space used:   144540
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 24 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