Alignments for a candidate for citF in Cronobacter muytjensii ATCC 51329

GapMind for catabolism of small carbon sources

Alignments for a candidate for citF in Cronobacter muytjensii ATCC 51329

Align Citrate lyase alpha chain; Citrase alpha chain; Citrate (pro-3S)-lyase alpha chain; Citrate CoA-transferase subunit; EC 4.1.3.6; EC 2.8.3.10 (characterized)
to candidate WP_038867774.1 AFK63_RS01780 citrate lyase subunit alpha

Query= SwissProt::P75726
         (510 letters)



>NCBI__GCF_001277195.1:WP_038867774.1
          Length = 505

 Score =  648 bits (1672), Expect = 0.0
 Identities = 329/490 (67%), Positives = 390/490 (79%), Gaps = 3/490 (0%)

Query: 24  DLAAFQNSPKQT---YQAEKARDRKLCANLEEAIRRSGLQDGMTVSFHHAFRGGDLTVNM 80
           DLA F  +   T      E    RKLCA+LEEA+R++GL+DGMT+SFHHAFR GD  +N 
Sbjct: 16  DLAPFDTAHTATPWLADNECKHTRKLCASLEEAVRKTGLRDGMTISFHHAFREGDRVINQ 75

Query: 81  VMDVIAKMGFKNLTLASSSLSDCHAPLVEHIRQGVVTRIYTSGLRGPLAEEISRGLLAEP 140
           V+  +A+MGFKNLTLASSSL  C+ PL+EHIR GV+TRIYTSG+RG LAE +S GL+AEP
Sbjct: 76  VVATLAQMGFKNLTLASSSLMTCNDPLIEHIRSGVITRIYTSGMRGKLAEAVSHGLMAEP 135

Query: 141 VQIHSHGGRVHLVQSGELNIDVAFLGVPSCDEFGNANGYTGKACCGSLGYAIVDADNAKQ 200
           VQIHSHGGRV L+Q GEL IDVAFLGVP  DE+GNANG  GK+CCGSLGYA+VDA  A+ 
Sbjct: 136 VQIHSHGGRVRLLQDGELAIDVAFLGVPCSDEYGNANGSHGKSCCGSLGYAMVDAQFARN 195

Query: 201 VVMLTEELLPYPHNPASIEQDQVDLIVKVDRVGDAAKIGAGATRMTTNPRELLIARSAAD 260
           VV+LTE L+PYP+ PAS+ QD+VD +V V+ VGD AKI  GA R+T+NPREL+IAR AAD
Sbjct: 196 VVLLTETLVPYPNMPASLSQDRVDFVVPVESVGDPAKISVGAARVTSNPRELMIARYAAD 255

Query: 261 VIVNSGYFKEGFSMQTGTGGASLAVTRFLEDKMRSRDIRADFALGGITATMVDLHEKGLI 320
           VI ++GYF +GFS+QTG+G AS A TRFL +KM    ++A FALGGIT ++VDLHEKGLI
Sbjct: 256 VIEHAGYFNDGFSIQTGSGAASTACTRFLGEKMARCGVKARFALGGITGSLVDLHEKGLI 315

Query: 321 RKLLDVQSFDSHAAQSLARNPNHIEISANQYANWGSKGASVDRLDVVVLSALEIDTQFNV 380
             LLD Q FDS AA SLARNP HIEIS N YA+  SK A  D+LD+V+LSALEID  FNV
Sbjct: 316 DVLLDTQCFDSQAAASLARNPKHIEISTNVYASPASKAACCDKLDMVILSALEIDVGFNV 375

Query: 381 NVLTGSDGVLRGASGGHCDTAIASALSIIVAPLVRGRIPTLVDNVLTCITPGSSVDILVT 440
           NV+TGSDGV+RGASGGHCD A A+ L+I+VAPL+R RIPT+V  V T +TPG S+D+LVT
Sbjct: 376 NVITGSDGVMRGASGGHCDVAAAANLTIVVAPLLRSRIPTVVKRVTTRLTPGESIDVLVT 435

Query: 441 DHGIAVNPARPELAERLQEAGIKVVSIEWLRERARLLTGEPQPIEFTDRVVAVVRYRDGS 500
           DHGIAVNPARPE+ ERL  AG+ VV I  L ERA  + GEP+PIEFTDR+V VVRYRDGS
Sbjct: 436 DHGIAVNPARPEVRERLVAAGLNVVDIHALCERAVAIAGEPKPIEFTDRIVGVVRYRDGS 495

Query: 501 VIDVVHQVKE 510
           VIDVV QVKE
Sbjct: 496 VIDVVRQVKE 505


Lambda     K      H
   0.319    0.134    0.384 

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: 796
Number of extensions: 26
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: 510
Length of database: 505
Length adjustment: 34
Effective length of query: 476
Effective length of database: 471
Effective search space:   224196
Effective search space used:   224196
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources