GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Herbaspirillum seropedicae SmR1

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate HSERO_RS05960 HSERO_RS05960 ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__HerbieS:HSERO_RS05960
          Length = 309

 Score =  156 bits (395), Expect = 5e-43
 Identities = 100/304 (32%), Positives = 177/304 (58%), Gaps = 25/304 (8%)

Query: 1   MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTF--- 57
           MDI  IQ I+NG+ +GS+ AL A+G T+ YG+L L NFAHGD L +GA +   +      
Sbjct: 1   MDI-FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQ 59

Query: 58  ---GVNIWLSMIVAVVGTVG----VMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRN 110
              G+   + +++A+VG +     V LL E++ +  +R+  A     +I +IG+++ L+ 
Sbjct: 60  VAPGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRN--APRLAPLITAIGVSILLQT 117

Query: 111 GIILIWGGRNQNYN--LPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKA 168
             ++IWG     +   +P  P + I G  +   Q+++LALAVL++  L  +++ TK+G+A
Sbjct: 118 LAMMIWGRSPLPFPQVMPSDP-VHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRA 176

Query: 169 MRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILPLF 227
           MRA A++  +A + G+D  +VI  T+ I   + ++ G M+    +  +  MG+   L  F
Sbjct: 177 MRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAF 236

Query: 228 ASVILGGIGNPYGAIAAAFIIGIVQ--------EVSTPFLGSQYKQGVALLIMILVLLIR 279
           ++ +LGGIGN YGA+    ++G+++        +++  FLGS Y+   A +++I+VL +R
Sbjct: 237 SAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLR 296

Query: 280 PKGL 283
           P G+
Sbjct: 297 PSGI 300


Lambda     K      H
   0.328    0.144    0.426 

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: 271
Number of extensions: 17
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: 288
Length of database: 309
Length adjustment: 27
Effective length of query: 261
Effective length of database: 282
Effective search space:    73602
Effective search space used:    73602
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