GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Magnetospirillum magneticum AMB-1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>NCBI__GCF_000009985.1:WP_011385357.1
          Length = 366

 Score =  183 bits (464), Expect = 7e-51
 Identities = 117/361 (32%), Positives = 178/361 (49%), Gaps = 12/361 (3%)

Query: 13  IAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKFE 72
           +AAA  +A A    + IG   P+SG++A +G+  + GA  A+E++NA+G  +G K     
Sbjct: 11  LAAALLMAGAARADITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGGVLGQK---LA 67

Query: 73  LVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNPN 132
           L   DDA DPKQ  A A ++   KV  V GH  SG++IPAS+VY + GI  ++ A+TNP 
Sbjct: 68  LTLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQISPASTNPK 127

Query: 133 LTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTATAK 192
            T+ G    FR    D+  G   A Y     K K VAI+ D++AYG+G+AD  +      
Sbjct: 128 FTERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQTRDALGKA 187

Query: 193 GMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYFG 252
           G+K    +  +    D+ A++T +KA   D +++GG   + G ++RQ+   GM   +  G
Sbjct: 188 GIKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGM-QTRLMG 246

Query: 253 GDGICTSEIAKL--AAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310
           GD + T E   +  AAG  T+         S   +     A   KY      + + Y+ Y
Sbjct: 247 GDALVTEEYWAITGAAGEGTMMTF------SPDPRKNPANADLVKYYRAQKYEPEAYTLY 300

Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370
           TY        A ++A + D K     L    F      I F+  G++  P   +YV+K G
Sbjct: 301 TYGTIQAWAQAAEKAKTTDWKKVAAVLKAEKFDTAIGKIGFDAKGDVAAPGYVMYVWKGG 360

Query: 371 K 371
           K
Sbjct: 361 K 361


Lambda     K      H
   0.315    0.131    0.375 

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: 382
Number of extensions: 14
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: 375
Length of database: 366
Length adjustment: 30
Effective length of query: 345
Effective length of database: 336
Effective search space:   115920
Effective search space used:   115920
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:

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