GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-sorbitol, ATPase component (characterized)
to candidate PfGW456L13_1799 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= reanno::pseudo6_N2E2:Pf6N2E2_1960
         (365 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1799
          Length = 351

 Score =  248 bits (632), Expect = 2e-70
 Identities = 144/327 (44%), Positives = 202/327 (61%), Gaps = 14/327 (4%)

Query: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60
           M+ L +EN++K +     +K ++L + + + V F+GPSGCGK+TLLR+IAGLE ++ G I
Sbjct: 1   MSGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120
            LDG DI       R+  MVFQ+ AL+PHMTV +N+++ L L G  K D + +V E   +
Sbjct: 61  RLDGEDIGHTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL 120

Query: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180
           ++L ++++R   +LSGGQRQRVAI RAI  +PKI L DEPLS LDA LR   ++E+ +L 
Sbjct: 121 IQLQAMINRPVAKLSGGQRQRVAIARAIANHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG 240
           + L  T I VTHDQ EAMT+A  VVVL   +++Q+G+P+E+Y HPAN FVA F+G+  + 
Sbjct: 181 QRLNITTIMVTHDQREAMTMADIVVVLGEHKVQQVGTPIEIYRHPANEFVADFIGSGNI- 239

Query: 241 FLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLSAEGQVPVTT 300
              ATV        +V    G  L +P  SS + VG+ V + IRPE L LSA    P  T
Sbjct: 240 -FPATV----LGNGKVSLPGGDALQVPICSS-IVVGEKVKMLIRPEDLQLSA----PQAT 289

Query: 301 DVTERLGSDTFCHVNVDSGESLTVRVQ 327
                LG  TF     D G ++   V+
Sbjct: 290 AGNRLLGKVTFVR---DIGATIETTVE 313


Lambda     K      H
   0.319    0.135    0.380 

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: 301
Number of extensions: 8
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: 365
Length of database: 351
Length adjustment: 29
Effective length of query: 336
Effective length of database: 322
Effective search space:   108192
Effective search space used:   108192
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