GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Herbaspirillum seropedicae SmR1

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate HSERO_RS14705 HSERO_RS14705 ABC transporter

Query= TCDB::Q8DQH8
         (254 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS14705 HSERO_RS14705 ABC
           transporter
          Length = 253

 Score =  248 bits (633), Expect = 9e-71
 Identities = 127/251 (50%), Positives = 171/251 (68%), Gaps = 1/251 (0%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           LL++  ++K+FGGL  +  V   + +GE+ GLIGPNGAGKTT+FNL+TG+   S G++  
Sbjct: 2   LLQLNDISKNFGGLQVLQGVNFNVRQGEIFGLIGPNGAGKTTVFNLITGLLRASSGSIRF 61

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
           +   +   +P+KI   G+ RTFQNIR+FK++T+L+NV++   +H    V +  L L  F 
Sbjct: 62  NDDDIGAVAPHKITERGIARTFQNIRVFKEMTLLENVVVGMHDHLNYGVASMLLNLGGFR 121

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
            +EKE + +ALELL    LD  A  LA +LSYG+QR+LE  RALAT+PK+L LDEP AGM
Sbjct: 122 NAEKEARERALELLSWVRLDHKAHMLADSLSYGEQRKLEFARALATKPKLLLLDEPVAGM 181

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242
           NP E  EL   I  IK     TI +IEHDM  VM + ERI VL +G++IA+GTPD+IK N
Sbjct: 182 NPAEKTELMSEIVNIKQR-GFTIFMIEHDMRFVMGLCERIAVLNFGKIIAEGTPDQIKNN 240

Query: 243 KRVIEAYLGGE 253
           + VIEAYLG E
Sbjct: 241 QEVIEAYLGKE 251


Lambda     K      H
   0.319    0.139    0.385 

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: 183
Number of extensions: 5
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: 254
Length of database: 253
Length adjustment: 24
Effective length of query: 230
Effective length of database: 229
Effective search space:    52670
Effective search space used:    52670
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 (21.7 bits)
S2: 47 (22.7 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