GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Herbaspirillum seropedicae SmR1

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 HSERO_RS05960 HSERO_RS05960 ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__HerbieS:HSERO_RS05960
          Length = 309

 Score =  249 bits (635), Expect = 8e-71
 Identities = 131/304 (43%), Positives = 196/304 (64%), Gaps = 15/304 (4%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMM--G 64
           ++QQ++NGL +GS YALIA+GYTMVYG++ +INFAHG++ M+G+ +    + ++  +  G
Sbjct: 4   FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPG 63

Query: 65  LDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLS 124
           L  + + ++ A   +I V       IER+AYRPLR   RL PLI+AIG+SI LQ   M+ 
Sbjct: 64  LPGI-VQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMI 122

Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184
                   P ++P + V     + G +IS  QI++  +  L M GL L + ++++GRA R
Sbjct: 123 WGRSPLPFPQVMPSDPVH----IAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMR 178

Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244
           A AE+ ++  L+G+++N +I +TF IGA LAA+A V+    Y      +GF+ G+KAF+A
Sbjct: 179 ATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSA 238

Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGD--------QYKDVVAFGLLILVLLFRPT 296
           AVLGGIG+I GAMLGG+LLG+ E+ GA   GD         Y+D+ AF +LI+VL  RP+
Sbjct: 239 AVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPS 298

Query: 297 GILG 300
           GI+G
Sbjct: 299 GIMG 302


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: 311
Number of extensions: 16
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: 307
Length of database: 309
Length adjustment: 27
Effective length of query: 280
Effective length of database: 282
Effective search space:    78960
Effective search space used:    78960
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