GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Herbaspirillum seropedicae SmR1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS05960 HSERO_RS05960 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__HerbieS:HSERO_RS05960
          Length = 309

 Score =  252 bits (643), Expect = 9e-72
 Identities = 133/302 (44%), Positives = 193/302 (63%), Gaps = 9/302 (2%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M+ F+QQ++NGL LGS+Y L+A+GYTMVYG++ +INFAHGDI M+G    L +  V+  +
Sbjct: 1   MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
             GLP  V L++ +V A+ +  + +  IER+AYRPLR + RLAPLITAIG+SI L     
Sbjct: 61  APGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAM 120

Query: 121 VTQGPRNKPIPP-MVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
           +  G    P P  M S         +S  QI+++ +  + +     IV +T +GRA RAT
Sbjct: 121 MIWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRAT 180

Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239
            ++ ++A L+GV+ ++ I +TF +GA LAA+AG M+   Y  A F  GF PG+KAF+AAV
Sbjct: 181 AENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAV 240

Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVLIFKPTGI 291
           LGGIG++ GA+ GG+L+GLIESL + Y            Y+D+  F +L  VL  +P+GI
Sbjct: 241 LGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGI 300

Query: 292 LG 293
           +G
Sbjct: 301 MG 302


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: 349
Number of extensions: 18
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: 300
Length of database: 309
Length adjustment: 27
Effective length of query: 273
Effective length of database: 282
Effective search space:    76986
Effective search space used:    76986
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 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