GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Sinorhizobium meliloti 1021

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate SMc02120 SMc02120 general L-amino acid transport permease ABC transporter protein

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Smeli:SMc02120
          Length = 384

 Score =  582 bits (1501), Expect = e-171
 Identities = 285/384 (74%), Positives = 321/384 (83%), Gaps = 1/384 (0%)

Query: 1   MSVADKPFVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVN 60
           MS     FVR S++ A P P  E GAV+W+R+NL ATPKD  LTI++L ++AW VP  + 
Sbjct: 1   MSTNQASFVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQ 60

Query: 61  WLFIQAVWSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIV 120
           WLFI A WSG  R  CAT  QGG QP+GWSGACWAF++AK+ QF+FGRYPL ERWRPA+V
Sbjct: 61  WLFIDAAWSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALV 120

Query: 121 GILFILLLVPMLIPSAPRKGLNAILLFAVLPVIAFWLLHGG-FGLEVVETPLWGGLMVTL 179
           GILF+LLLVPMLIP  P KGLNA+LL   LP+++  LL GG FGL  VETPLWGGLMVTL
Sbjct: 121 GILFVLLLVPMLIPRIPYKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTL 180

Query: 180 VLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLP 239
           VLSFVGIAVSLP+GILLALGRRS MPVI+MLC  FIEVIRGVPLITVLFMASVMLPLFLP
Sbjct: 181 VLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLP 240

Query: 240 TGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQ 299
            G   DK LRALIGVS+F SAYMAEV+RGGLQAIPKGQ+EGADSLGL +WQK   I++PQ
Sbjct: 241 QGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQ 300

Query: 300 AIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFI 359
           A+KLVIP IVNTFIG FKDTSLV+IIGMFDLLGIV+LNFSD NWA+AVTP+TGLIFAGF+
Sbjct: 301 ALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFV 360

Query: 360 FWLFCFGMSRYSGFMERHLDTGHK 383
           FWLFCFGMSRYSGFMER LD   +
Sbjct: 361 FWLFCFGMSRYSGFMERLLDRSQR 384


Lambda     K      H
   0.330    0.145    0.469 

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: 693
Number of extensions: 25
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: 384
Length of database: 384
Length adjustment: 30
Effective length of query: 354
Effective length of database: 354
Effective search space:   125316
Effective search space used:   125316
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: 50 (23.9 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