GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_011384081.1 AMB_RS08460 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_000009985.1:WP_011384081.1
          Length = 315

 Score =  176 bits (446), Expect = 9e-49
 Identities = 106/325 (32%), Positives = 177/325 (54%), Gaps = 25/325 (7%)

Query: 85  LSLPSTQRWAVLALVVVAFVWPF-FASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLG 143
           ++L + +   + AL +V  + P  F++    D+    +   +L +GLN+++G AG + LG
Sbjct: 1   MNLKTARTGGLAALAIVITLAPLGFSNSYFYDVGVNAMFNAILCVGLNLLIGYAGQISLG 60

Query: 144 YVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGF 203
           + GF+A+GAY   +L E  G     AL ++  +  +  F++  P+L+L+G YLA+ TLG 
Sbjct: 61  HAGFFALGAYGSGILTERYGVPAIGALVLSASVVGILAFVVARPILKLKGHYLAMATLGI 120

Query: 204 GEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVI 263
           G II I+L+    ITGGP+G+ S+    + G T      +G Q                 
Sbjct: 121 GIIIHIVLKTEAGITGGPDGM-SLGNFKMLGFTI-----KGDQ----------------- 157

Query: 264 LLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASF 323
           + Y V  +L++LA+++   L+  P+GRA  A+   EV    +G++ +  K+  F + A F
Sbjct: 158 MWYWVTGVLLVLAVWLSLNLIESPVGRALRAVHGSEVGAEVVGVDTSSYKVLVFVVSAVF 217

Query: 324 AGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL-QEMRGF 382
           A   GS FA + G +TP+  +F  S  ++ +VVLGGM S  G ++ AV++ LL Q +   
Sbjct: 218 ASVVGSLFAHKNGFITPDISSFFHSVELVTMVVLGGMASIYGALIGAVILTLLPQVLAAV 277

Query: 383 NEYRMLIFGLTMIVMMIWRPQGLLP 407
            +Y  +I G  M+  MI+ P+GLLP
Sbjct: 278 EQYEAMILGAIMMGTMIFMPKGLLP 302


Lambda     K      H
   0.330    0.146    0.439 

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: 373
Number of extensions: 23
Number of successful extensions: 4
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: 417
Length of database: 315
Length adjustment: 29
Effective length of query: 388
Effective length of database: 286
Effective search space:   110968
Effective search space used:   110968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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