GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Herbaspirillum seropedicae SmR1

Align RhaQ (characterized, see rationale)
to candidate HSERO_RS22210 HSERO_RS22210 branched-chain amino acid ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__HerbieS:HSERO_RS22210
          Length = 339

 Score =  338 bits (868), Expect = 9e-98
 Identities = 176/330 (53%), Positives = 239/330 (72%), Gaps = 2/330 (0%)

Query: 1   MSTVSTQPEKRI-IPDRLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDA 59
           M+  ++ P  R  I ++     R +   WE LL  + VL+   N L  P+F D +NL+D+
Sbjct: 4   MNEPASPPRSRYRIDEKARFQPRDLLRHWEALLAILLVLVCAVNGLLLPHFFDPYNLADS 63

Query: 60  TFNFTEKAMIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGL 119
           TFNF+EKAMIA  MALL+I  EID+SV+AIIALAS AMG A Q G+   GL+L+ I TG 
Sbjct: 64  TFNFSEKAMIALPMALLIICREIDISVSAIIALASVAMGLANQAGVPPLGLLLVAIATGT 123

Query: 120 ACGVFNGVLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVF 179
           ACG+ NG LV+ L LPSIVVTIG+MSLFRG++ +VLGDQA+ +YP     +GQGY   V 
Sbjct: 124 ACGLLNGALVTRLGLPSIVVTIGSMSLFRGLASVVLGDQAFTQYPEVLGDWGQGYFFDVL 183

Query: 180 SFEFVLFIVLAVLFAILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSG 239
              FV++++ AV+FA+LLH T +GR++YAIGNN  AARFSG+ V+R +  LF+LTG M+G
Sbjct: 184 PRPFVVWLLAAVVFAVLLHVTRWGRRLYAIGNNPVAARFSGVAVDRYRLALFVLTGAMAG 243

Query: 240 IAAVCLTSRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFG 299
           +AA  LT R+GSTRP+IA GWELE++T+V+LGG+SI GG     GV +++  VMG++T+G
Sbjct: 244 LAAFFLTGRIGSTRPNIAMGWELEIITVVILGGVSIAGGTGSIGGV-MLSVLVMGMLTYG 302

Query: 300 LGLLNLPGIVMSIFIGLLIIVTIAIPIIAR 329
           L L N+PGI+M+I +G L++ TIAIP + R
Sbjct: 303 LALANIPGIIMTIVVGALLLATIAIPRLLR 332



 Score = 25.4 bits (54), Expect = 0.002
 Identities = 17/74 (22%), Positives = 34/74 (45%)

Query: 76  LVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLP 135
           + +  E+++    I+   S A G     G+    LV+  +  GLA     G++++++   
Sbjct: 260 IAMGWELEIITVVILGGVSIAGGTGSIGGVMLSVLVMGMLTYGLALANIPGIIMTIVVGA 319

Query: 136 SIVVTIGTMSLFRG 149
            ++ TI    L RG
Sbjct: 320 LLLATIAIPRLLRG 333


Lambda     K      H
   0.330    0.145    0.423 

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: 371
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 337
Length of database: 339
Length adjustment: 28
Effective length of query: 309
Effective length of database: 311
Effective search space:    96099
Effective search space used:    96099
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: 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