GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Lactobacillus silagei IWT126

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_054655217.1 CES79_RS10005 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_002217945.1:WP_054655217.1
          Length = 292

 Score =  233 bits (593), Expect = 5e-66
 Identities = 133/303 (43%), Positives = 182/303 (60%), Gaps = 14/303 (4%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAAL--IVFLVLT 58
           M    QQL+NGL+LGSIY L+A+GYTMVYGII +INFAHGDI+MLG F     I +    
Sbjct: 1   MTTLFQQLINGLSLGSIYALLALGYTMVYGIIKLINFAHGDIYMLGAFWGYYTINYWHFN 60

Query: 59  SIFAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNF 118
            IFA           L+ AM++ +     IE  AYRPLR + R+  LITAIG+S  L N 
Sbjct: 61  FIFA-----------LLSAMVVCAASGVIIEYFAYRPLRHAPRITALITAIGVSYFLENG 109

Query: 119 IQVTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQR 177
           +    G   +  P ++  V Y    + VS  QI+I+    +L+ +   I+ +T +GRA R
Sbjct: 110 MSYLYGADTRDFPQVIKQVNYSLWGVRVSNIQILILATACLLMILLQLIIKKTKMGRAMR 169

Query: 178 ATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTA 237
           A   D   A L+G+N++QTIS TF +G+++A  AG +  +YY       G TPG+KAF A
Sbjct: 170 AVSVDPDAAELVGININQTISFTFALGSSMAGAAGVLIGLYYNSIDPLMGMTPGIKAFVA 229

Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297
           AV+GGIGS+PGA  GG LIGL+E+   +    AYKD A + +L  +L+  P+GI G+   
Sbjct: 230 AVVGGIGSVPGASLGGFLIGLLETAVQSVGLSAYKDAAVYLVLIIILLVLPSGIFGKNVK 289

Query: 298 EKV 300
           EKV
Sbjct: 290 EKV 292


Lambda     K      H
   0.329    0.143    0.421 

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: 323
Number of extensions: 22
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: 300
Length of database: 292
Length adjustment: 26
Effective length of query: 274
Effective length of database: 266
Effective search space:    72884
Effective search space used:    72884
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 (21.8 bits)
S2: 48 (23.1 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