GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ga0059261_1577 in Caulobacter crescentus NA1000

Align L-glutamine and L-histidine transporter (characterized)
to candidate CCNA_01242 CCNA_01242 amino acid permease

Query= reanno::Korea:Ga0059261_1577
         (470 letters)



>FitnessBrowser__Caulo:CCNA_01242
          Length = 531

 Score =  334 bits (857), Expect = 4e-96
 Identities = 206/528 (39%), Positives = 289/528 (54%), Gaps = 66/528 (12%)

Query: 1   MAGG-LFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIG-VGAGKAGP 58
           MAG  LF  K +    ++A   +L  TL   +L++LGVGAI+G GI  L G V +  AGP
Sbjct: 1   MAGNRLFLKKSIASIQKEAAHSQLKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGP 60

Query: 59  AVIMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLV 118
           A+++SF++AG  CA A L YAE+A+ MP SGSAY Y+Y  LGE+ AW++GW L+LEY + 
Sbjct: 61  AIMLSFIVAGIACALAGLCYAELASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVA 120

Query: 119 VSTVAVGWSGYAAPLLHA-----------------WTGMPLELMAGPHA------NGIVN 155
            STVAVGWSGY    LHA                 W    ++ +A P         G +N
Sbjct: 121 ASTVAVGWSGYVVSTLHALGINFPMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLN 180

Query: 156 LPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPF--APF 213
           L A   IA+V+ LL +G  ESA +N A+VV+K+I L  F+AV   Y N AN  PF   P 
Sbjct: 181 LVAAIGIAMVSALLVVGVSESANVNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPEPT 240

Query: 214 GFAKTISPDGVERGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAI 273
           G        G+ RG    AAIIFFA+ GF+A+STAA E KNP RD+ IGI+G++I C  I
Sbjct: 241 GQPGEFGIGGIFRG----AAIIFFAYVGFEAVSTAAAEAKNPSRDVPIGILGALIICTLI 296

Query: 274 YMLVAVAAVGATPFTHFANSPEPLALILRDL--------------GRPGFATF-LAVSAI 318
           YM VA    G  PF   A SP P+A+ +  +              G+    +F + + AI
Sbjct: 297 YMAVAAVMTGVVPFRELA-SPAPIAVAIDRMGLEWADIPYAAAEGGKLNLLSFAIKIGAI 355

Query: 319 IALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-SKRGSPVRITLFTAAIVAVIAGLLP 377
             L +V+L   +GQ+RIF+TMARDG+LP   A++  K  +P   T+    ++A+ A  LP
Sbjct: 356 TGLSSVMLVLCYGQTRIFYTMARDGLLPKVFAEIHPKFRTPWLGTILLGVVIAIAASFLP 415

Query: 378 IDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFS- 436
           I  +  L + GT  AF+ V + ++ LR++ PD+PR F+ P      A  +  C++L +  
Sbjct: 416 ISLLGDLVSLGTAVAFSIVCLSVIYLRIKHPDLPRPFKVPGGIFTAAAGIAACLFLPYQN 475

Query: 437 -------------LPVKTQLWFLAWNALGVVIYFAYARPRVS-AKGIE 470
                        LP+   +    + A+G +IY AY       AKGI+
Sbjct: 476 FQPMIVHAMNDNPLPL---MILGGYAAVGAIIYIAYGYWHSKLAKGID 520


Lambda     K      H
   0.327    0.140    0.426 

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: 729
Number of extensions: 44
Number of successful extensions: 7
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: 470
Length of database: 531
Length adjustment: 34
Effective length of query: 436
Effective length of database: 497
Effective search space:   216692
Effective search space used:   216692
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 (21.7 bits)
S2: 52 (24.6 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