GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapM in Pseudomonas stutzeri RCH2

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 GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52814
         (384 letters)



>lcl|FitnessBrowser__psRCH2:GFF3102 Psest_3161 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 365

 Score =  385 bits (990), Expect = e-112
 Identities = 197/367 (53%), Positives = 251/367 (68%), Gaps = 14/367 (3%)

Query: 18  PPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCA 77
           PPP    GA+ W+R NL ++  + +LT++ L L+   VP ++ W   +A W+G  R  C+
Sbjct: 11  PPPTISIGALGWLRANLFSSWINTLLTLVGLYLLWLIVPPVLEWAIFKADWTGETRADCS 70

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

Query: 138 RKGLNAILLFAVLPVIAFWLLHGGF-GLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILL 196
            K    I    V P++A+WLLHGGF GL+ V T  WGGLM+T+V++ VGIA +LP+GILL
Sbjct: 120 HKLRYGIGYLLVYPLLAYWLLHGGFLGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILL 179

Query: 197 ALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSI 256
           ALGRRS MP IR+LCVTFIE  RGVPLITVLFM+SVMLPLFLP G N+DKLLRA++ V  
Sbjct: 180 ALGRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNLDKLLRAMLMVVF 239

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

Query: 317 KDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMER 376
           KDTSLV IIG+FD L  +K   +D  W    T   G +FA  ++W+FCFGMSRYS  +ER
Sbjct: 300 KDTSLVIIIGLFDFLNSIKRATADPAWLGMST--EGYVFAALVYWMFCFGMSRYSMRLER 357

Query: 377 HLDTGHK 383
            LDTGHK
Sbjct: 358 KLDTGHK 364


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: 577
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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