GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Marinobacter adhaerens HP15

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  322 bits (824), Expect = 1e-92
 Identities = 173/369 (46%), Positives = 245/369 (66%), Gaps = 16/369 (4%)

Query: 1   MSELQLSDVRKSYGGL--EVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSG 58
           MS+L+L  +RK+Y G+  E +KG+D+DI SGEF++ VGPSGCGKSTL+  IAGLE I+ G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  DLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAA 118
            + +D   ++ ++P  R IAMVFQSYALYP M+VREN+ F L+  G+P+ EI++ V   A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 HILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIAR 178
            +L++  L+++KP  LSGGQ+QRVA+GRA+ R P+I+LFDEPLSNLDA+LRV MR EI +
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPK 238
           LH++L TTIVYVTHDQ+EAMTLAD+I V++ G ++Q+G+P ++YD P NLFVAGF+GSP 
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 239 MNFLKGVIEIDED--QAYARLPDYGDAKIPVT--LQAAAGTAVTIGIRPEHF-------- 286
           M+F+   +E  E   QA  R  D    K+PV   L    G  V +GIRPEH         
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300

Query: 287 DEAGPAALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSV 346
           D+   A  +  I++ E  G +  A  + +       ++ ++   +  G+     FD   V
Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEH--PVTWGETAELMFDMKKV 358

Query: 347 LVFDGEGKR 355
           + FD E ++
Sbjct: 359 VFFDPETEK 367


Lambda     K      H
   0.321    0.139    0.396 

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: 415
Number of extensions: 16
Number of successful extensions: 3
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: 358
Length of database: 372
Length adjustment: 30
Effective length of query: 328
Effective length of database: 342
Effective search space:   112176
Effective search space used:   112176
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: 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