GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas stutzeri RCH2

Align ABC transporter for D-sorbitol, ATPase component (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit

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



>FitnessBrowser__psRCH2:GFF3591
          Length = 369

 Score =  232 bits (591), Expect = 1e-65
 Identities = 125/292 (42%), Positives = 186/292 (63%), Gaps = 10/292 (3%)

Query: 4   LKIENLKKGFEGLS-IIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIEL 62
           +    ++K ++G S I++ ++L+++  EF+  +GPSG GK+T L ++AG E  T+G I L
Sbjct: 11  VSFRGIQKSYDGESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILL 70

Query: 63  DGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILE 122
           DGR I  V P KRD+ MVFQ YAL+PHMTV +NL+F L + G  KPD++ +V  A  +++
Sbjct: 71  DGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQ 130

Query: 123 LGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKE 182
           L    +R P QLSGGQ+QRVA+ RA+V  P++ L DEPL  LD  LR Q ++E+  LH+ 
Sbjct: 131 LEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHER 190

Query: 183 LQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFL 242
           L  T++YVTHDQ EA+T++ +V V + G+I+QI  P  LY  P N FVA FLG  +   L
Sbjct: 191 LGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLG--ENNRL 248

Query: 243 QATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQS---VTIGIRPEHLTLS 291
            A +         V+   G T+    ++ A++VG +   V++ IRPE + L+
Sbjct: 249 PAHLLDRRGDSCTVKLGRGETV----EALAVNVGAAGTPVSLSIRPERVLLN 296


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: 337
Number of extensions: 10
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 365
Length of database: 369
Length adjustment: 30
Effective length of query: 335
Effective length of database: 339
Effective search space:   113565
Effective search space used:   113565
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