GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_011385948.1 AMB_RS18170 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_000009985.1:WP_011385948.1
          Length = 297

 Score =  143 bits (361), Expect = 4e-39
 Identities = 95/306 (31%), Positives = 161/306 (52%), Gaps = 21/306 (6%)

Query: 8   LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67
           LQ LVNGL VG+ Y ++A+ + ++Y    ++NFA GE  +IG++  +  +T        S
Sbjct: 7   LQLLVNGLIVGTLYGVVAMCFVLIYKSTQVVNFAQGEFLLIGAWTCWWLVT--------S 58

Query: 68  VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDS 127
           + L    AF  + +    FG +++ +  RPL G   +  ++  IG+SIF Q  +      
Sbjct: 59  MALPFYVAFPMTFLFMMVFGIALQMIVLRPLIGEPVISVIMVTIGLSIFFQAVMKSIFGV 118

Query: 128 KEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACA 187
             +  P + P   V     + G+ +    ++  VV+ ++M     F   SR+G A RA A
Sbjct: 119 WAQPFPEIFPVKSV----DILGLSVQPAYLMSLVVSIVIMGLFAWFFKYSRMGLAMRATA 174

Query: 188 EDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVL 247
            + ++   LGI+   + A  + I A ++A+A V++GM  GV +  + F  GIK F A ++
Sbjct: 175 FNQQVAQSLGISVKAVFATAWAISAMVSALAGVVVGMVNGV-SSALSFF-GIKVFPAVIV 232

Query: 248 GGIGSIPGAMLGGLLLGVAEAFGADVFGDQY------KDVVAFGLLILVLLFRPTGILGR 301
           GG+ SI GA+LGGL++GV E   A+    QY        V  F +L+++L+ +P G+ G 
Sbjct: 233 GGLDSIIGAVLGGLIIGVLENL-AEYADGQYLHLGNLYTVAPFYVLVIILMIKPYGLFGT 291

Query: 302 PEVEKV 307
             +E+V
Sbjct: 292 KTIERV 297


Lambda     K      H
   0.328    0.145    0.413 

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: 265
Number of extensions: 20
Number of successful extensions: 5
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: 307
Length of database: 297
Length adjustment: 27
Effective length of query: 280
Effective length of database: 270
Effective search space:    75600
Effective search space used:    75600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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