GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artP in Herbaspirillum seropedicae SmR1

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate HSERO_RS11450 HSERO_RS11450 ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS11450 HSERO_RS11450 ABC
           transporter ATP-binding protein
          Length = 257

 Score =  264 bits (675), Expect = 1e-75
 Identities = 139/245 (56%), Positives = 174/245 (71%), Gaps = 5/245 (2%)

Query: 1   MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60
           +++V  L KSFG H VLK++  ++A  +VV VIGPSGSGKSTFLRCLN LEK  GGT+ +
Sbjct: 5   IVEVSGLRKSFGAHVVLKDLDLSVAPSQVVVVIGPSGSGKSTFLRCLNGLEKAEGGTVKV 64

Query: 61  KDTEITK-----PKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQE 115
               + +     P+     +R  +GMVFQ F+LFPH TVL+NI  AP  ++  S++AAQ+
Sbjct: 65  CGRPVVEGGRMMPEAMLDLLRAEVGMVFQSFNLFPHLTVLDNITLAPTCLRGMSRKAAQQ 124

Query: 116 KAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEV 175
           +A  LL KVGL  K   YP  LSGGQKQRVAIARALAM P +MLFDEPTSALDPE+V EV
Sbjct: 125 QALQLLEKVGLAHKAKAYPGTLSGGQKQRVAIARALAMEPQVMLFDEPTSALDPELVGEV 184

Query: 176 LQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDF 235
           LQV++ L   GMTM+IVTHEMGFA+EVAD V+ MD G IVE G P   F +P+  R + F
Sbjct: 185 LQVIRALAAEGMTMIIVTHEMGFAREVADVVVVMDHGSIVEAGPPGAIFTAPQQARTRSF 244

Query: 236 LEKIL 240
           L+ +L
Sbjct: 245 LQTML 249


Lambda     K      H
   0.317    0.134    0.368 

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: 211
Number of extensions: 3
Number of successful extensions: 2
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: 240
Length of database: 257
Length adjustment: 24
Effective length of query: 216
Effective length of database: 233
Effective search space:    50328
Effective search space used:    50328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 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 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