GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Magnetospirillum magneticum AMB-1

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:G8ALI9
         (505 letters)



>NCBI__GCF_000009985.1:WP_011384209.1
          Length = 415

 Score =  473 bits (1216), Expect = e-138
 Identities = 256/461 (55%), Positives = 313/461 (67%), Gaps = 57/461 (12%)

Query: 16  SILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLVFLGRLGLCLIRE 75
           +++ +A +   VA  + +P++G+R  D  TGL L  R + VA A G V   RL + L+R 
Sbjct: 8   ALVVDALLGGVVAAAMALPMLGVRLEDGSTGLSLSGRLDWVAWAAGSVAGARLLIGLLRL 67

Query: 76  GHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRTGRSKLSQAERDK 135
           G              AG   ++P     +++  G A++A                     
Sbjct: 68  G-------------LAGRGPSLPAPPRAMMVYVGWAMVAF-------------------- 94

Query: 136 RMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGL 195
                                  AL  PF P + R L+D   L+L Y+MLGWGLNIVVGL
Sbjct: 95  -----------------------ALILPFLPFSGRNLVDKATLVLIYVMLGWGLNIVVGL 131

Query: 196 AGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYF 255
           AGLLDLG+VAFYAVGAYSYALL+  FG SFWVCLPLAG LAA  G++LGFPVLRLRGDY 
Sbjct: 132 AGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPLAGLLAAAFGMVLGFPVLRLRGDYI 191

Query: 256 AIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLE 315
           AIVT+G GEI+R++L NW   TGGPNGISGI RPS FG++ F   P EG+  F E FGL+
Sbjct: 192 AIVTMGLGEIVRVVLQNWQDVTGGPNGISGIERPSLFGLS-FKMVPPEGSQTFAEFFGLD 250

Query: 316 FSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLA 375
           +S  HR+IFLY+LIL LAL+ N+ T+R+R+LP+GRAWEALRED+IAC SLGIN T +KL+
Sbjct: 251 YSADHRVIFLYFLILALALLTNVITLRIRRLPVGRAWEALREDEIACRSLGINPTLVKLS 310

Query: 376 AFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIG 435
           AFA  AMF GFAGSFFATRQGFISPESFTFIESA+ILAIVVLGGMGSQIG+V+AA L++G
Sbjct: 311 AFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAIVVLGGMGSQIGIVLAALLLVG 370

Query: 436 LPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476
           LPE FREL  +RMLAFG  MVLIMLW+P GLL+ R+PTI L
Sbjct: 371 LPEWFRELQQFRMLAFGGAMVLIMLWKPAGLLSTREPTIRL 411


Lambda     K      H
   0.329    0.144    0.438 

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: 697
Number of extensions: 36
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 505
Length of database: 415
Length adjustment: 33
Effective length of query: 472
Effective length of database: 382
Effective search space:   180304
Effective search space used:   180304
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: 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