GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Herbaspirillum seropedicae SmR1

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate HSERO_RS08285 HSERO_RS08285 amino acid ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08285 HSERO_RS08285 amino acid
           ABC transporter ATP-binding protein
          Length = 258

 Score =  347 bits (890), Expect = e-100
 Identities = 164/252 (65%), Positives = 207/252 (82%)

Query: 3   REILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTI 62
           + +L+V NLSMRFGGLLAV+GV+L V+E++V A+IGPNGAGKTTVFNC++GFY+PT G I
Sbjct: 6   KTMLEVSNLSMRFGGLLAVDGVSLAVQEREVFAIIGPNGAGKTTVFNCISGFYRPTSGEI 65

Query: 63  LLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPA 122
           +LDG  I   P H +A++G+VRTFQN+RLFK MT VENLL+AQH+ +NTN  +GL KTPA
Sbjct: 66  MLDGASIARQPSHQVAQQGLVRTFQNIRLFKSMTVVENLLVAQHQQVNTNLLSGLLKTPA 125

Query: 123 FRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
           +RKSE+EA++ A YWLD++ LT  ANR AGTL+YG QRR+EIARCM+T+PR+L+LDEPAA
Sbjct: 126 YRKSEQEALQRAAYWLDQLGLTALANREAGTLSYGLQRRVEIARCMITKPRLLLLDEPAA 185

Query: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242
           GLNP+E ++L  LI  LR EH V VLLIEHDM L+M ISD I+V+  G P+  GTPEQ+R
Sbjct: 186 GLNPQEKQELSQLIDRLRREHGVAVLLIEHDMSLIMGISDRILVMEHGKPIVTGTPEQVR 245

Query: 243 DNPEVIKAYLGE 254
            +  VIKAYLGE
Sbjct: 246 SDERVIKAYLGE 257


Lambda     K      H
   0.321    0.138    0.398 

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: 233
Number of extensions: 4
Number of successful extensions: 1
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: 255
Length of database: 258
Length adjustment: 24
Effective length of query: 231
Effective length of database: 234
Effective search space:    54054
Effective search space used:    54054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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