GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citW in Pseudomonas fluorescens FW300-N2E3

Align citrate lyase holo-[acyl-carrier protein] synthase (EC 2.7.7.61) (characterized)
to candidate AO353_24495 AO353_24495 malate permease

Query= BRENDA::Q8VS41
         (454 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24495
          Length = 447

 Score =  320 bits (821), Expect = 5e-92
 Identities = 162/436 (37%), Positives = 266/436 (61%), Gaps = 4/436 (0%)

Query: 15  IDTPKTTLKQRWWHIMDNWKVGIVPLPLFLLAGGLIALDCLGGKLPSDIVVMVATLAFFG 74
           ID P+   + R    +  +++G++PLP+FL    ++ L    G LP++++  +A +   G
Sbjct: 11  IDAPRDG-RLRQLRSLCGYEIGVIPLPIFLGIAVIVYLSAHLGFLPNNMIGGLAVIMTMG 69

Query: 75  FACGEFGKRLPVLGKLGAAAICATFIPSALVHYGLLPDVVIESTTKFYKSTNILYLYICC 134
              G+ G RLP+L ++G  AI    +PS LV YG      I++T    K  N LY  I  
Sbjct: 70  MFFGQLGSRLPILKEIGGGAILCLMLPSILVFYGFFGPATIDATKMLMKEANFLYFVIAS 129

Query: 135 IIVGSIMSMNRTTLIQGFLKIFFPMLCGEVVGMLVGIGVGTLLGMEPFQVFFFIVLPIMA 194
           ++VGSI+ M+R  LIQG +++F P+L G +  +  G+ VG L+G   +  FFFI++PI+ 
Sbjct: 130 LVVGSILGMSRFILIQGMMRMFIPLLVGTLAAVASGLIVGKLVGYSFYHTFFFIIVPIIG 189

Query: 195 GGVGEGAIPLSMGYAALMHMEQGVALGRVLPMVMLGSLTAIVISGCLNQLGKRFPHLTGE 254
           GG+GEG +PLS+ Y+A++     + + +++P  ++G++ AI+ +G L +L  + PHL GE
Sbjct: 190 GGIGEGILPLSLAYSAILGGTPDIYVAKLVPAAVVGNIAAIICAGYLARLALKRPHLNGE 249

Query: 255 GQLMPNRSHETRSLSESEGVSGKT-DVGTLASGALLAVLLYMMGMLGHKLIGLPAPVGML 313
           G L+  R+ +     ++   +G T D   + +G L+    +++G L  K++G+P PV M+
Sbjct: 250 GSLI--RAKDENDKFQAREDNGSTIDFRVIGAGILVICAFFVLGGLLEKILGVPGPVLMI 307

Query: 314 FLAVLLKLANVVSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQELVNAFTLTNLLV 373
             AVL K   V+  +L++G+   YK   +A  +P++  +G+   P   +V  F+++ +LV
Sbjct: 308 LAAVLFKYIRVLPEKLEKGTNAFYKLISSAFIWPVMIGLGMLYVPLDSVVKVFSISYVLV 367

Query: 374 IVSTVSALVATGFLVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTAGNRMSLMPFAQIA 433
            VS V+++   GF +G  + M+PI+ AIV+CC SG GGTGDVAIL+A NRMSLMPFAQI+
Sbjct: 368 CVSVVASMAIAGFFIGNLMKMYPIESAIVTCCHSGLGGTGDVAILSASNRMSLMPFAQIS 427

Query: 434 TRIGGAINVSLGLLFL 449
           TR+GGA  V +  + L
Sbjct: 428 TRLGGASTVIIASILL 443


Lambda     K      H
   0.326    0.142    0.428 

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: 757
Number of extensions: 61
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: 454
Length of database: 447
Length adjustment: 33
Effective length of query: 421
Effective length of database: 414
Effective search space:   174294
Effective search space used:   174294
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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 (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