GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Caulobacter crescentus NA1000

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate CCNA_02366 CCNA_02366 cytoplasmic membrane maltose transporter malY

Query= TCDB::Q9A612
         (541 letters)



>FitnessBrowser__Caulo:CCNA_02366
          Length = 503

 Score =  998 bits (2579), Expect = 0.0
 Identities = 503/503 (100%), Positives = 503/503 (100%)

Query: 39  MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 98
           MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV
Sbjct: 1   MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 60

Query: 99  QPIIGHFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITM 158
           QPIIGHFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITM
Sbjct: 61  QPIIGHFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITM 120

Query: 159 EPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSV 218
           EPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSV
Sbjct: 121 EPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSV 180

Query: 219 RIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALG 278
           RIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALG
Sbjct: 181 RIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALG 240

Query: 279 VGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFSEVLADV 338
           VGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFSEVLADV
Sbjct: 241 VGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFSEVLADV 300

Query: 339 FRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAV 398
           FRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAV
Sbjct: 301 FRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAV 360

Query: 399 YNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWS 458
           YNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWS
Sbjct: 361 YNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWS 420

Query: 459 SILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLG 518
           SILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLG
Sbjct: 421 SILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLG 480

Query: 519 ALSFALAAAATFLVRDRVAGAPA 541
           ALSFALAAAATFLVRDRVAGAPA
Sbjct: 481 ALSFALAAAATFLVRDRVAGAPA 503


Lambda     K      H
   0.327    0.140    0.437 

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: 1074
Number of extensions: 33
Number of successful extensions: 1
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: 541
Length of database: 503
Length adjustment: 35
Effective length of query: 506
Effective length of database: 468
Effective search space:   236808
Effective search space used:   236808
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: 52 (24.6 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