GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Pseudomonas fluorescens FW300-N2C3

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 AO356_17390 AO356_17390 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17390
          Length = 365

 Score =  398 bits (1022), Expect = e-115
 Identities = 203/368 (55%), Positives = 251/368 (68%), Gaps = 14/368 (3%)

Query: 18  PPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCA 77
           PPP    G VAW+R N+ ++  + +LT+ A  LI   VP L+ W  + A W G  R  C 
Sbjct: 11  PPPSSSIGVVAWMRANMFSSWLNTLLTLFAFYLIYLIVPPLLQWAILDANWVGTTRADCT 70

Query: 78  TTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAP 137
                        GACW FI  ++ QF++G YP   RWR  +     +L + P+ I   P
Sbjct: 71  K-----------EGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWAAVLGVAPLFISRFP 119

Query: 138 RKGLNAILLFAVLPVIAFWLLHGG-FGLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILL 196
           RK +  +    + P+IA+ LLHGG FGL+ V T  WGGLM+TLV++ VGI  +LP+GI+L
Sbjct: 120 RKAIYGLSFLVLYPIIAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVL 179

Query: 197 ALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSI 256
           ALGRRS MP IR++CVTFIE  RGVPLITVLFM+SVMLPLFLP G N DKLLRALIGV +
Sbjct: 180 ALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVIL 239

Query: 257 FTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTF 316
           F SAY+AEV+RGGLQAIPKGQ+E A ++GLGYW+   L+I+PQA+KLVIP IVNTFI  F
Sbjct: 240 FQSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALF 299

Query: 317 KDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMER 376
           KDTSLV IIG+FDLL  VK   +D  W    T   G +FA  +FW+FCFGMSRYS  +ER
Sbjct: 300 KDTSLVIIIGLFDLLNSVKQAAADPKWLGMAT--EGYVFAALVFWIFCFGMSRYSMHLER 357

Query: 377 HLDTGHKR 384
            LDTGHKR
Sbjct: 358 KLDTGHKR 365


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: 581
Number of extensions: 28
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: 384
Length of database: 365
Length adjustment: 30
Effective length of query: 354
Effective length of database: 335
Effective search space:   118590
Effective search space used:   118590
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