Aligments for a candidate for Ga0059261_1577 in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Aligments for a candidate for Ga0059261_1577 in Caulobacter crescentus NA1000

Align L-glutamine and L-histidine transporter (characterized)
to candidate CCNA_00435 CCNA_00435 amino acid transporter

Query= reanno::Korea:Ga0059261_1577
         (470 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00435 CCNA_00435 amino acid
           transporter
          Length = 483

 Score =  528 bits (1360), Expect = e-154
 Identities = 273/450 (60%), Positives = 334/450 (74%), Gaps = 6/450 (1%)

Query: 15  AEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMSFVIAGAICACA 74
           A  A  H+L  TLSWPHLVALGVGAIVGTGI TL GVGAG AGP VI+SF+IAGA+CACA
Sbjct: 22  AGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGLAGPGVILSFLIAGAVCACA 81

Query: 75  ALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAPLL 134
           AL YAE++TM+PASGSAY YSYA +GE +AW VGWSLILEY+LV + VAVGWS +A  L 
Sbjct: 82  ALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLF 141

Query: 135 HAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVF 194
               G P  L+AGPH  G++N+PA+FI   VAGLL LGT+ESAT+N  LV VKIIAL VF
Sbjct: 142 -KMIGFPDALLAGPHQGGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIALIVF 200

Query: 195 VAVALPYFNGANLEPFAPFGFAKTI----SPDGVERGVMAAAAIIFFAFYGFDAISTAAE 250
           V + LP FN A+  PF P GF   +    + D  + GVMAAA++IFFAFYGFDA+STAAE
Sbjct: 201 VVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYGFDAVSTAAE 260

Query: 251 ETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILRDLGRPGFA 310
           ETKNP RDL IGIVGSM  C AIYM+VA  ++GA+    F+ S  PL  IL  L     A
Sbjct: 261 ETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFILESLNHGKIA 320

Query: 311 TFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-SKRGSPVRITLFTAAIV 369
             +A++A+IALPTV+L F++GQSRIFF MARDG+LP  L+KV +K G+PV +TL T  + 
Sbjct: 321 QLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGVLA 380

Query: 370 AVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLG 429
           AVI+GLL + +IA LANAGTL AF AV   +++LR+R P+ PR+F TPLW +V    +LG
Sbjct: 381 AVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLWPIVAPAGILG 440

Query: 430 CIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459
           C+YLF SLP KTQL+FL  + +G V+Y AY
Sbjct: 441 CLYLFLSLPGKTQLYFLYAHLIGAVVYLAY 470


Lambda     K      H
   0.327    0.140    0.426 

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: 708
Number of extensions: 36
Number of successful extensions: 4
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: 470
Length of database: 483
Length adjustment: 33
Effective length of query: 437
Effective length of database: 450
Effective search space:   196650
Effective search space used:   196650
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:

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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