GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Pseudomonas putida KT2440

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate PP_1299 PP_1299 putative amino acid ABC transporter - membrane subunit

Query= reanno::Smeli:SMc02120
         (384 letters)



>FitnessBrowser__Putida:PP_1299
          Length = 365

 Score =  397 bits (1019), Expect = e-115
 Identities = 204/367 (55%), Positives = 251/367 (68%), Gaps = 13/367 (3%)

Query: 18  PAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCA 77
           P P    G ++W+R NLF++  +T LT+ ++ ++  +VPP +QW  IDA W G  R  C 
Sbjct: 11  PPPVKTVGVLAWMRANLFSSWLNTLLTLFAIYLVWLIVPPLLQWALIDANWVGTTRADCT 70

Query: 78  TLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVPMLIPRIP 137
                        GACW FV  +F QF++G YP + RWR  L   L VL   P+ I R P
Sbjct: 71  K-----------EGACWVFVQQRFGQFMYGYYPTELRWRVDLTVWLAVLGAAPLFIKRFP 119

Query: 138 YKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILL 197
            K    L  LV  P+L+  LL GG+ GL  V T  WGGLM+TLV++ VGI  +LPLGILL
Sbjct: 120 RKAFYGLGFLVLYPVLAYTLLHGGYLGLESVPTSQWGGLMLTLVIATVGIVGALPLGILL 179

Query: 198 ALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSL 257
           ALGRRS MP +K++C  FIE  RGVPLITVLFM+SVMLPLFLP+G++FDK LRA+IGV L
Sbjct: 180 ALGRRSRMPAVKVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMSFDKLLRAMIGVIL 239

Query: 258 FASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLF 317
           F SAY+AEVVRGGLQAIPKGQYE A ++GL +W+ MG ++LPQALKLVIPGIVNTFI LF
Sbjct: 240 FQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALF 299

Query: 318 KDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMER 377
           KDTSLV IIG+FDLL  V+   +D  W    T   G +FA  VFW+FCFGMSRYS  +ER
Sbjct: 300 KDTSLVIIIGLFDLLNSVKQAAADPAWLGMAT--EGYVFAALVFWIFCFGMSRYSMHLER 357

Query: 378 LLDRSQR 384
            LD   +
Sbjct: 358 KLDTGHK 364


Lambda     K      H
   0.329    0.144    0.454 

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: 571
Number of extensions: 24
Number of successful extensions: 3
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