GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Catellicoccus marimammalium M35/04/3

Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate WP_009490041.1 C683_RS03460 amino acid permease

Query= TCDB::M1IW84
         (556 letters)



>NCBI__GCF_000313915.1:WP_009490041.1
          Length = 479

 Score =  271 bits (694), Expect = 3e-77
 Identities = 156/425 (36%), Positives = 237/425 (55%), Gaps = 25/425 (5%)

Query: 17  LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPA-VMVVYGIIGFFVFFVLRAMGEL 75
           ++R L  RH+ +IAIGG+IGTGLF+ SG  IS AGP   +V YG+IG  VFF++ ++GE+
Sbjct: 8   MQRGLKTRHLSMIAIGGSIGTGLFVASGSAISTAGPGGALVAYGLIGLLVFFMMTSLGEM 67

Query: 76  LLSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPIWV 135
                   SF  +A   + PA GF +GW+YWF W +T   D+        +W+P +P W+
Sbjct: 68  ATYMPVSGSFSTYATKFVDPAFGFALGWNYWFNWAITLAVDISTSAIIMEYWFPDVPGWI 127

Query: 136 PALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHATI 195
            +++   LI  +NL SV  FGE EFWF++IKV  ++C I VG +L  T  +  H     +
Sbjct: 128 FSIIFFVLIFLMNLASVELFGEAEFWFSMIKVITVICFIGVG-LLTVTGILGGHA--DGL 184

Query: 196 ENLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLRVA 255
            N    +  F  G   +VS F +A F++ GVE++G  A E+A+P +++P+AI  V  R+ 
Sbjct: 185 MNFTKGDAPFVGGLPTIVSVFVVAGFSFQGVEMIGITAGESANPEKSIPKAIKQVFWRIL 244

Query: 256 VFYIGALLAILAVVPWRQ--------FASGESPFVTMFSLAGLAAAASVVNFVVVTAAAS 307
           +FY+ ++  I  ++P+               SPF  +F  AGLAAAASV+N V++T+  S
Sbjct: 245 LFYLVSIFIIGLIIPYTSPNLLGSDATDIAISPFTLVFQRAGLAAAASVMNAVILTSVLS 304

Query: 308 SANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVI 367
           + NSG ++  RML  +A  G AP AF ++NR G+P  ALLLTA +   +    + G  + 
Sbjct: 305 AGNSGLYAGARMLCAMAQSGQAPKAFQKINRRGIPVNALLLTAAVGGLAFITSFMGDKI- 363

Query: 368 GAFTLVTTVSSLLFMFVWAMIIISYLVYRRRH-PQRHTDSVYK-----MPGG----VVMC 417
             +  + + S L     W  + +S+  +RR    Q H  S  K      P G    ++MC
Sbjct: 364 --YNFLLSASGLTGFIAWFGVAVSHYRFRRAFIKQGHDISELKYKSKWFPFGPIFAIIMC 421

Query: 418 WAVLV 422
            AV+V
Sbjct: 422 IAVIV 426


Lambda     K      H
   0.328    0.140    0.442 

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: 629
Number of extensions: 39
Number of successful extensions: 5
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: 556
Length of database: 479
Length adjustment: 35
Effective length of query: 521
Effective length of database: 444
Effective search space:   231324
Effective search space used:   231324
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 (21.8 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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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